Query 032449
Match_columns 140
No_of_seqs 110 out of 625
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 14:14:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032449.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032449hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1984 Vesicle coat complex C 100.0 4.3E-35 9.3E-40 265.2 8.4 107 18-124 268-374 (1007)
2 COG5028 Vesicle coat complex C 100.0 1.6E-30 3.4E-35 233.6 5.5 104 19-125 133-236 (861)
3 KOG1985 Vesicle coat complex C 99.9 4.1E-27 8.8E-32 212.8 4.8 91 31-124 164-254 (887)
4 PLN00162 transport protein sec 99.9 4.7E-26 1E-30 207.9 8.2 86 35-127 7-92 (761)
5 PTZ00395 Sec24-related protein 99.9 6E-25 1.3E-29 206.3 3.8 125 5-134 623-756 (1560)
6 KOG1986 Vesicle coat complex C 99.8 2.7E-20 5.9E-25 166.6 2.9 97 33-136 5-101 (745)
7 COG5047 SEC23 Vesicle coat com 99.7 1.1E-18 2.5E-23 154.2 3.7 97 34-137 6-103 (755)
8 PF04810 zf-Sec23_Sec24: Sec23 99.7 5.4E-19 1.2E-23 106.8 1.0 39 87-125 1-39 (40)
9 COG2888 Predicted Zn-ribbon RN 90.3 0.11 2.3E-06 34.0 0.5 32 78-119 28-59 (61)
10 TIGR01053 LSD1 zinc finger dom 89.2 0.35 7.6E-06 27.5 2.0 29 89-121 2-30 (31)
11 PF13719 zinc_ribbon_5: zinc-r 88.5 0.31 6.8E-06 28.4 1.6 33 88-120 2-35 (37)
12 PF10058 DUF2296: Predicted in 88.2 0.37 8E-06 30.7 1.9 34 87-120 21-54 (54)
13 PF09082 DUF1922: Domain of un 87.8 0.37 8E-06 32.3 1.8 30 88-123 3-32 (68)
14 PRK00398 rpoP DNA-directed RNA 85.7 0.63 1.4E-05 28.1 1.8 31 88-122 3-33 (46)
15 PRK14890 putative Zn-ribbon RN 83.9 0.5 1.1E-05 30.8 0.8 28 82-119 30-57 (59)
16 smart00661 RPOL9 RNA polymeras 83.1 0.74 1.6E-05 28.0 1.4 32 90-123 2-33 (52)
17 PF02318 FYVE_2: FYVE-type zin 80.2 1.3 2.7E-05 32.0 1.9 32 88-119 71-103 (118)
18 PRK03954 ribonuclease P protei 79.1 1.4 2.9E-05 32.6 1.8 37 89-125 65-108 (121)
19 PF13717 zinc_ribbon_4: zinc-r 78.0 1.4 3E-05 25.6 1.3 32 88-119 2-34 (36)
20 PF09723 Zn-ribbon_8: Zinc rib 75.8 1.3 2.9E-05 26.4 0.8 30 89-119 6-35 (42)
21 COG5415 Predicted integral mem 74.0 2 4.3E-05 35.0 1.6 51 88-138 192-245 (251)
22 PF08271 TF_Zn_Ribbon: TFIIB z 73.7 3.9 8.5E-05 24.2 2.5 27 90-119 2-28 (43)
23 PRK12380 hydrogenase nickel in 73.3 2.3 5E-05 30.6 1.7 28 87-120 69-96 (113)
24 cd00350 rubredoxin_like Rubred 73.3 2.2 4.8E-05 24.1 1.3 24 90-119 3-26 (33)
25 TIGR02605 CxxC_CxxC_SSSS putat 72.2 1.9 4.2E-05 26.3 0.9 31 89-120 6-36 (52)
26 TIGR00100 hypA hydrogenase nic 72.1 2.6 5.6E-05 30.4 1.7 28 87-120 69-96 (115)
27 PF11781 RRN7: RNA polymerase 71.9 3 6.5E-05 24.3 1.6 27 88-119 8-34 (36)
28 PF10122 Mu-like_Com: Mu-like 71.7 1.5 3.2E-05 27.8 0.3 36 89-126 5-40 (51)
29 cd00730 rubredoxin Rubredoxin; 70.9 1.6 3.5E-05 27.3 0.4 30 90-119 3-43 (50)
30 PF08792 A2L_zn_ribbon: A2L zi 69.2 7.1 0.00015 22.3 2.8 30 87-120 2-31 (33)
31 PF09779 Ima1_N: Ima1 N-termin 69.2 3.1 6.7E-05 30.7 1.6 34 89-124 1-34 (131)
32 PRK03681 hypA hydrogenase nick 68.7 3.5 7.6E-05 29.7 1.8 29 87-120 69-97 (114)
33 PRK12722 transcriptional activ 68.6 2.2 4.8E-05 33.7 0.8 31 85-118 131-162 (187)
34 smart00834 CxxC_CXXC_SSSS Puta 68.5 2.5 5.3E-05 24.3 0.8 29 89-118 6-34 (41)
35 COG1096 Predicted RNA-binding 66.1 3.7 8.1E-05 32.5 1.6 27 88-120 149-175 (188)
36 PF14803 Nudix_N_2: Nudix N-te 64.1 2.2 4.8E-05 24.6 -0.0 29 91-119 3-31 (34)
37 COG1996 RPC10 DNA-directed RNA 62.8 4.2 9.1E-05 25.5 1.1 31 88-122 6-36 (49)
38 PF07282 OrfB_Zn_ribbon: Putat 62.8 5.3 0.00012 25.6 1.6 29 88-120 28-56 (69)
39 PF07754 DUF1610: Domain of un 61.5 7.3 0.00016 20.9 1.7 24 91-118 1-24 (24)
40 PF13240 zinc_ribbon_2: zinc-r 61.0 3.7 8.1E-05 21.5 0.5 21 90-118 1-21 (23)
41 smart00132 LIM Zinc-binding do 60.8 7.7 0.00017 21.2 1.9 29 90-118 1-35 (39)
42 PF12760 Zn_Tnp_IS1595: Transp 59.6 11 0.00024 22.6 2.5 27 89-118 19-45 (46)
43 PF00641 zf-RanBP: Zn-finger i 59.0 3.1 6.8E-05 22.7 0.0 13 110-122 4-16 (30)
44 PRK00564 hypA hydrogenase nick 58.9 4.2 9.1E-05 29.4 0.7 29 87-120 70-98 (117)
45 TIGR00311 aIF-2beta translatio 58.6 16 0.00035 27.2 3.8 33 88-123 97-131 (133)
46 PF01927 Mut7-C: Mut7-C RNAse 57.5 8.1 0.00018 28.7 2.0 33 88-120 91-134 (147)
47 PF06943 zf-LSD1: LSD1 zinc fi 57.5 11 0.00023 20.5 1.9 24 91-118 1-24 (25)
48 TIGR01384 TFS_arch transcripti 56.1 7.6 0.00016 26.9 1.6 27 90-122 2-28 (104)
49 PF02891 zf-MIZ: MIZ/SP-RING z 55.7 0.86 1.9E-05 28.3 -3.0 32 87-118 14-49 (50)
50 PF00301 Rubredoxin: Rubredoxi 55.6 3.1 6.7E-05 25.7 -0.4 30 90-119 3-43 (47)
51 TIGR02098 MJ0042_CXXC MJ0042 f 54.8 9.8 0.00021 21.6 1.7 31 89-119 3-34 (38)
52 COG2956 Predicted N-acetylgluc 54.6 7.4 0.00016 33.8 1.5 36 86-129 352-387 (389)
53 PF13894 zf-C2H2_4: C2H2-type 53.5 6.9 0.00015 19.0 0.8 10 111-120 1-10 (24)
54 PF13408 Zn_ribbon_recom: Reco 53.5 8.8 0.00019 23.3 1.4 32 86-118 3-34 (58)
55 PRK00432 30S ribosomal protein 52.6 7.5 0.00016 24.2 1.0 25 89-119 21-46 (50)
56 COG0675 Transposase and inacti 52.4 7.8 0.00017 30.9 1.3 24 88-120 309-332 (364)
57 PF04032 Rpr2: RNAse P Rpr2/Rp 52.3 9.7 0.00021 25.1 1.6 31 88-118 46-85 (85)
58 cd00729 rubredoxin_SM Rubredox 52.2 7.5 0.00016 22.2 0.8 11 110-120 2-12 (34)
59 smart00401 ZnF_GATA zinc finge 51.6 7.4 0.00016 24.2 0.8 32 88-119 3-34 (52)
60 COG1592 Rubrerythrin [Energy p 51.1 8.4 0.00018 29.9 1.2 14 107-120 131-144 (166)
61 PF13831 PHD_2: PHD-finger; PD 51.0 2.3 5.1E-05 24.7 -1.4 32 86-117 2-36 (36)
62 PF06827 zf-FPG_IleRS: Zinc fi 50.1 9 0.00019 20.8 0.9 27 90-118 3-29 (30)
63 KOG2846 Predicted membrane pro 49.6 12 0.00027 32.0 2.1 36 88-123 220-255 (328)
64 smart00659 RPOLCX RNA polymera 49.3 16 0.00034 22.1 2.0 25 90-119 4-28 (44)
65 TIGR00416 sms DNA repair prote 49.1 8.7 0.00019 33.9 1.2 30 87-124 6-35 (454)
66 PRK03824 hypA hydrogenase nick 48.4 12 0.00026 27.7 1.6 34 87-120 69-117 (135)
67 smart00547 ZnF_RBZ Zinc finger 48.2 7.1 0.00015 20.4 0.3 13 110-122 2-14 (26)
68 PF12773 DZR: Double zinc ribb 48.1 7.1 0.00015 23.4 0.3 30 87-121 11-40 (50)
69 PRK00762 hypA hydrogenase nick 48.0 9.2 0.0002 27.9 1.0 33 87-120 69-102 (124)
70 PRK12860 transcriptional activ 47.6 9.4 0.0002 30.3 1.0 30 85-117 131-161 (189)
71 PF05280 FlhC: Flagellar trans 46.5 7 0.00015 30.4 0.1 31 85-118 131-162 (175)
72 PF10571 UPF0547: Uncharacteri 46.3 8.1 0.00018 20.9 0.4 23 90-120 2-24 (26)
73 PRK11823 DNA repair protein Ra 46.2 9.6 0.00021 33.4 1.0 29 88-124 7-35 (446)
74 cd02342 ZZ_UBA_plant Zinc fing 46.0 14 0.0003 22.6 1.4 22 89-117 1-22 (43)
75 COG2051 RPS27A Ribosomal prote 43.7 27 0.00058 23.3 2.5 33 88-123 19-51 (67)
76 PF03604 DNA_RNApol_7kD: DNA d 43.2 16 0.00034 20.8 1.3 13 85-97 14-26 (32)
77 COG2023 RPR2 RNase P subunit R 42.3 14 0.00031 26.6 1.2 37 89-125 57-97 (105)
78 PF00320 GATA: GATA zinc finge 42.3 8.1 0.00018 22.2 -0.1 28 91-118 1-28 (36)
79 PF12874 zf-met: Zinc-finger o 42.2 15 0.00033 18.5 1.0 10 111-120 1-10 (25)
80 PF14353 CpXC: CpXC protein 41.2 28 0.00061 24.9 2.6 23 87-109 37-62 (128)
81 PF02150 RNA_POL_M_15KD: RNA p 40.3 27 0.00059 19.9 2.0 30 90-122 3-32 (35)
82 PRK06393 rpoE DNA-directed RNA 39.7 17 0.00036 24.0 1.1 23 88-120 5-27 (64)
83 PRK03988 translation initiatio 38.8 53 0.0011 24.6 3.9 34 88-124 102-137 (138)
84 KOG3799 Rab3 effector RIM1 and 37.1 21 0.00045 27.3 1.5 31 87-121 88-118 (169)
85 COG0375 HybF Zn finger protein 36.9 25 0.00054 25.7 1.8 28 87-120 69-96 (115)
86 PRK14810 formamidopyrimidine-D 36.3 32 0.00069 28.2 2.5 28 89-118 245-272 (272)
87 PF00130 C1_1: Phorbol esters/ 36.3 28 0.0006 20.9 1.7 29 86-119 9-37 (53)
88 smart00249 PHD PHD zinc finger 35.8 23 0.0005 19.8 1.2 31 86-116 12-47 (47)
89 PF15288 zf-CCHC_6: Zinc knuck 35.5 14 0.0003 22.2 0.2 11 89-99 2-12 (40)
90 PRK08270 anaerobic ribonucleos 35.0 18 0.00039 33.6 1.0 25 86-119 624-648 (656)
91 PF05129 Elf1: Transcription e 34.6 14 0.00031 25.1 0.2 14 109-122 21-34 (81)
92 PRK12336 translation initiatio 34.6 57 0.0012 25.7 3.6 33 88-123 98-132 (201)
93 PF10263 SprT-like: SprT-like 34.5 23 0.0005 25.8 1.3 31 86-118 121-151 (157)
94 COG4888 Uncharacterized Zn rib 33.9 20 0.00043 25.9 0.8 14 109-122 21-34 (104)
95 PF13453 zf-TFIIB: Transcripti 33.2 29 0.00063 20.2 1.4 11 87-97 18-28 (41)
96 PRK05580 primosome assembly pr 33.1 52 0.0011 30.5 3.6 38 88-125 381-423 (679)
97 PF01155 HypA: Hydrogenase exp 32.6 14 0.0003 26.5 -0.2 28 87-120 69-96 (113)
98 PRK11827 hypothetical protein; 32.5 41 0.00089 21.8 2.1 33 87-123 7-39 (60)
99 cd02338 ZZ_PCMF_like Zinc fing 31.9 26 0.00056 21.4 1.0 22 89-117 1-22 (49)
100 PF00412 LIM: LIM domain; Int 31.5 73 0.0016 19.0 3.1 28 88-116 26-53 (58)
101 PF13597 NRDD: Anaerobic ribon 31.3 27 0.00059 31.6 1.5 26 86-120 489-514 (546)
102 PHA00626 hypothetical protein 31.3 48 0.001 21.5 2.2 30 86-125 9-38 (59)
103 PF08274 PhnA_Zn_Ribbon: PhnA 31.0 26 0.00057 19.6 0.9 27 88-119 2-28 (30)
104 PF08879 WRC: WRC; InterPro: 30.9 23 0.0005 21.8 0.7 9 106-114 10-18 (46)
105 PRK08351 DNA-directed RNA poly 30.8 24 0.00052 23.0 0.8 21 90-120 5-25 (61)
106 PRK14811 formamidopyrimidine-D 30.7 57 0.0012 26.7 3.1 32 90-123 237-268 (269)
107 cd02340 ZZ_NBR1_like Zinc fing 30.1 38 0.00082 20.2 1.5 21 89-117 1-21 (43)
108 PRK01103 formamidopyrimidine/5 30.0 50 0.0011 26.9 2.7 27 90-118 247-273 (274)
109 PRK08271 anaerobic ribonucleos 29.3 23 0.0005 32.8 0.7 27 86-120 564-590 (623)
110 PRK12286 rpmF 50S ribosomal pr 29.3 43 0.00093 21.3 1.8 26 86-120 25-50 (57)
111 TIGR00686 phnA alkylphosphonat 28.8 50 0.0011 24.0 2.2 29 88-121 2-30 (109)
112 PRK08402 replication factor A; 28.3 43 0.00094 28.8 2.1 44 87-136 211-262 (355)
113 TIGR01031 rpmF_bact ribosomal 27.9 41 0.0009 21.2 1.5 24 87-119 25-48 (55)
114 TIGR00595 priA primosomal prot 27.9 54 0.0012 29.2 2.8 20 106-125 236-255 (505)
115 smart00778 Prim_Zn_Ribbon Zinc 27.8 66 0.0014 18.8 2.2 12 107-118 22-33 (37)
116 PRK07111 anaerobic ribonucleos 27.7 30 0.00065 32.6 1.1 25 86-119 678-702 (735)
117 KOG3399 Predicted Yippee-type 27.7 23 0.0005 26.3 0.3 25 87-113 14-38 (122)
118 PF06397 Desulfoferrod_N: Desu 27.4 29 0.00063 20.3 0.6 13 108-120 4-16 (36)
119 KOG2169 Zn-finger transcriptio 27.1 30 0.00065 32.0 1.0 42 86-127 317-362 (636)
120 PRK00420 hypothetical protein; 27.1 39 0.00084 24.6 1.4 29 89-122 24-52 (112)
121 PF05907 DUF866: Eukaryotic pr 26.9 51 0.0011 25.2 2.1 35 88-122 30-76 (161)
122 PF00569 ZZ: Zinc finger, ZZ t 26.9 53 0.0012 19.6 1.8 22 89-117 5-26 (46)
123 PRK00415 rps27e 30S ribosomal 26.5 81 0.0018 20.5 2.7 33 88-123 11-43 (59)
124 PRK07218 replication factor A; 25.9 34 0.00074 30.2 1.1 27 86-122 295-321 (423)
125 COG4416 Com Mu-like prophage p 25.8 12 0.00026 24.2 -1.3 33 88-122 4-36 (60)
126 PF13465 zf-H2C2_2: Zinc-finge 25.7 43 0.00093 17.5 1.1 12 108-119 12-23 (26)
127 KOG4784 Uncharacterized conser 25.7 24 0.00052 30.5 0.1 35 85-120 181-215 (348)
128 cd04476 RPA1_DBD_C RPA1_DBD_C: 25.6 57 0.0012 24.2 2.2 27 88-120 34-61 (166)
129 PHA02942 putative transposase; 25.5 43 0.00092 28.9 1.6 29 87-120 324-352 (383)
130 PF02591 DUF164: Putative zinc 25.4 21 0.00046 22.1 -0.2 29 90-118 24-54 (56)
131 PRK13130 H/ACA RNA-protein com 25.1 77 0.0017 20.3 2.4 27 87-123 4-30 (56)
132 COG1773 Rubredoxin [Energy pro 25.1 42 0.0009 21.5 1.1 17 102-118 28-44 (55)
133 cd00202 ZnF_GATA Zinc finger D 24.9 15 0.00032 23.1 -1.0 28 91-118 2-29 (54)
134 PRK13945 formamidopyrimidine-D 24.6 65 0.0014 26.5 2.5 26 90-117 256-281 (282)
135 PF14692 DUF4462: Domain of un 24.6 26 0.00056 19.5 0.1 13 41-53 5-17 (28)
136 COG1198 PriA Primosomal protei 24.6 96 0.0021 29.4 3.8 43 86-132 442-484 (730)
137 KOG1074 Transcriptional repres 24.4 31 0.00066 33.3 0.6 42 82-123 347-394 (958)
138 smart00290 ZnF_UBP Ubiquitin C 23.8 57 0.0012 19.2 1.5 21 90-120 1-21 (50)
139 COG1594 RPB9 DNA-directed RNA 23.6 52 0.0011 23.7 1.5 34 89-124 3-36 (113)
140 PF09788 Tmemb_55A: Transmembr 23.5 1.3E+02 0.0027 25.1 3.9 38 85-124 62-99 (256)
141 PRK04351 hypothetical protein; 23.5 84 0.0018 23.7 2.7 31 87-119 111-141 (149)
142 PF00096 zf-C2H2: Zinc finger, 23.5 49 0.0011 16.1 1.0 10 111-120 1-10 (23)
143 TIGR00354 polC DNA polymerase, 23.5 43 0.00093 32.9 1.3 27 86-122 623-649 (1095)
144 PF05715 zf-piccolo: Piccolo Z 23.2 37 0.00081 22.2 0.6 19 109-128 29-47 (61)
145 COG0266 Nei Formamidopyrimidin 23.1 58 0.0013 27.2 1.9 28 89-118 246-273 (273)
146 TIGR00375 conserved hypothetic 22.8 25 0.00053 30.6 -0.4 32 84-119 236-267 (374)
147 PRK14892 putative transcriptio 22.8 79 0.0017 22.4 2.3 33 87-120 20-52 (99)
148 COG1645 Uncharacterized Zn-fin 22.7 66 0.0014 24.1 1.9 25 89-119 29-53 (131)
149 PF12172 DUF35_N: Rubredoxin-l 22.4 56 0.0012 18.4 1.2 25 87-119 10-34 (37)
150 KOG4623 Uncharacterized conser 22.3 31 0.00067 31.5 0.2 34 87-124 27-61 (611)
151 cd02344 ZZ_HERC2 Zinc finger, 22.2 63 0.0014 19.7 1.5 22 89-117 1-22 (45)
152 COG3677 Transposase and inacti 21.8 41 0.00088 24.8 0.7 36 88-123 30-66 (129)
153 PF03966 Trm112p: Trm112p-like 21.8 20 0.00043 23.1 -0.9 17 106-122 49-65 (68)
154 PF06677 Auto_anti-p27: Sjogre 21.6 79 0.0017 18.9 1.8 24 89-117 18-41 (41)
155 COG2093 DNA-directed RNA polym 21.4 36 0.00078 22.5 0.3 23 89-119 5-27 (64)
156 COG2260 Predicted Zn-ribbon RN 21.4 62 0.0013 21.1 1.4 26 88-123 5-30 (59)
157 PF04981 NMD3: NMD3 family ; 21.2 74 0.0016 25.4 2.1 20 86-106 33-52 (236)
158 PF06524 NOA36: NOA36 protein; 21.2 54 0.0012 27.7 1.3 16 103-118 135-150 (314)
159 COG0846 SIR2 NAD-dependent pro 21.2 54 0.0012 26.9 1.4 18 87-104 145-163 (250)
160 PRK12366 replication factor A; 20.9 72 0.0016 29.5 2.2 29 86-120 530-558 (637)
161 PRK05452 anaerobic nitric oxid 20.8 44 0.00096 29.6 0.8 35 85-119 422-467 (479)
162 smart00704 ZnF_CDGSH CDGSH-typ 20.4 1.2E+02 0.0025 17.7 2.3 18 105-123 9-26 (38)
163 PF04959 ARS2: Arsenite-resist 20.3 46 0.001 26.8 0.8 25 96-121 64-88 (214)
164 COG1545 Predicted nucleic-acid 20.0 80 0.0017 23.4 2.0 25 88-120 29-53 (140)
No 1
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.3e-35 Score=265.21 Aligned_cols=107 Identities=52% Similarity=1.115 Sum_probs=104.0
Q ss_pred CCCCCCCceeEecccCCCCCCeeEeeccccCCCHHHHhhcCCCeEEEEeeccCCCCCCCCCceeccCCCCeeecCCCCcE
Q 032449 18 KPPPPVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGY 97 (140)
Q Consensus 18 ~~pp~~~~~~~~~d~gn~~p~~vR~T~~~iP~t~~l~~~~~iPlgivv~Pf~~~~~~e~~vp~v~~~~~~~~RC~~C~aY 97 (140)
..||++||+|++.|||||+|+|||+|+|.||.|.++++.++||||+||+||+.+.+.|+++|+||+++.+++||+||+||
T Consensus 268 ~~PPl~TTd~~~~DqGN~sPr~mr~T~Y~iP~T~Dl~~as~iPLalvIqPfa~l~p~E~~~~vVd~g~sgPvRC~RCkaY 347 (1007)
T KOG1984|consen 268 QPPPLVTTDFFIQDQGNCSPRFMRCTMYTIPCTNDLLKASQIPLALVIQPFATLTPNEAPVPVVDLGESGPVRCNRCKAY 347 (1007)
T ss_pred CCCCCcccceEEeccCCCCcchheeecccCCccHhHHHhcCCcceeEecccccCCcccCCCceecCCCCCCcchhhhhhh
Confidence 36999999999999999999999999999999999999999999999999999988888999999999999999999999
Q ss_pred EcCceeEEeCCcEEEEccCCCCCCCCC
Q 032449 98 RNPFMEFVDNGKSFVCNFCGVWMLMRG 124 (140)
Q Consensus 98 iNPf~~~~~~g~~w~C~lC~~~N~lp~ 124 (140)
||||++|+++||+|+||||+.+|.+|.
T Consensus 348 inPFmqF~~~gr~f~Cn~C~~~n~vp~ 374 (1007)
T KOG1984|consen 348 INPFMQFIDGGRKFICNFCGSKNQVPD 374 (1007)
T ss_pred cCcceEEecCCceEEecCCCccccCCh
Confidence 999999999999999999999999984
No 2
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=99.96 E-value=1.6e-30 Score=233.58 Aligned_cols=104 Identities=37% Similarity=0.773 Sum_probs=96.3
Q ss_pred CCCCCCceeEecccCCCCCCeeEeeccccCCCHHHHhhcCCCeEEEEeeccCCCCCCCCCceeccCCCCeeecCCCCcEE
Q 032449 19 PPPPVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYR 98 (140)
Q Consensus 19 ~pp~~~~~~~~~d~gn~~p~~vR~T~~~iP~t~~l~~~~~iPlgivv~Pf~~~~~~e~~vp~v~~~~~~~~RC~~C~aYi 98 (140)
.||. ++.++..+++||+|+|||+|+|+||.+.+++++++||||+||+||.++.++|.++|++.. ..|+||++||+||
T Consensus 133 ~ppl-tt~~~~~e~~n~~p~yvrsT~yaiP~t~dl~~~skiPfgLVI~Pf~~l~~e~~~vpl~~d--~~ivRCrrCrsYi 209 (861)
T COG5028 133 VPPL-TTNFVGSEQSNCSPKYVRSTMYAIPETNDLLKKSKIPFGLVIRPFLELYPEEDPVPLVED--GSIVRCRRCRSYI 209 (861)
T ss_pred CCCc-ccceeeeccCCCCHHHHHHHHhhCCCchhHHHhcCCCceEEeehhhhcCccCCCCccCCC--CcchhhhhhHhhc
Confidence 4665 999999999999999999999999999999999999999999999998887777888763 3489999999999
Q ss_pred cCceeEEeCCcEEEEccCCCCCCCCCC
Q 032449 99 NPFMEFVDNGKSFVCNFCGVWMLMRGL 125 (140)
Q Consensus 99 NPf~~~~~~g~~w~C~lC~~~N~lp~~ 125 (140)
|||.+|+++|++|+||+|+.+|.+|.-
T Consensus 210 NPfv~fi~~g~kw~CNiC~~kN~vp~~ 236 (861)
T COG5028 210 NPFVQFIEQGRKWRCNICRSKNDVPEG 236 (861)
T ss_pred CceEEEecCCcEEEEeeccccccCccc
Confidence 999999999999999999999999963
No 3
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.93 E-value=4.1e-27 Score=212.78 Aligned_cols=91 Identities=44% Similarity=0.868 Sum_probs=83.0
Q ss_pred ccCCCCCCeeEeeccccCCCHHHHhhcCCCeEEEEeeccCCCCCCCCCceeccCCCCeeecCCCCcEEcCceeEEeCCcE
Q 032449 31 DTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKS 110 (140)
Q Consensus 31 d~gn~~p~~vR~T~~~iP~t~~l~~~~~iPlgivv~Pf~~~~~~e~~vp~v~~~~~~~~RC~~C~aYiNPf~~~~~~g~~ 110 (140)
..-||+|+|||+|+++||++.++++|+|||||++|+||++.+ ++.++|++. ...|+||++||+|||||+.|++.|++
T Consensus 164 ~~~nc~p~y~RsTl~~iP~t~sLl~kskLPlglvv~Pf~~~~-d~~~~p~~~--~~~IvRCr~CRtYiNPFV~fid~gr~ 240 (887)
T KOG1985|consen 164 ESSNCSPSYVRSTLSAIPQTQSLLKKSKLPLGLVVHPFAHLD-DIDPLPVIT--STLIVRCRRCRTYINPFVEFIDQGRR 240 (887)
T ss_pred cccCCCHHHHHHHHHhCCccHHHHHhcCCCceEEEeeccccc-ccCCCCccc--CCceeeehhhhhhcCCeEEecCCCce
Confidence 457999999999999999999999999999999999999876 334566664 57899999999999999999999999
Q ss_pred EEEccCCCCCCCCC
Q 032449 111 FVCNFCGVWMLMRG 124 (140)
Q Consensus 111 w~C~lC~~~N~lp~ 124 (140)
|+||+|+..|.+|.
T Consensus 241 WrCNlC~~~NdvP~ 254 (887)
T KOG1985|consen 241 WRCNLCGRVNDVPD 254 (887)
T ss_pred eeechhhhhcCCcH
Confidence 99999999999995
No 4
>PLN00162 transport protein sec23; Provisional
Probab=99.93 E-value=4.7e-26 Score=207.85 Aligned_cols=86 Identities=23% Similarity=0.309 Sum_probs=79.1
Q ss_pred CCCCeeEeeccccCCCHHHHhhcCCCeEEEEeeccCCCCCCCCCceeccCCCCeeecCCCCcEEcCceeEEeCCcEEEEc
Q 032449 35 CSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKSFVCN 114 (140)
Q Consensus 35 ~~p~~vR~T~~~iP~t~~l~~~~~iPlgivv~Pf~~~~~~e~~vp~v~~~~~~~~RC~~C~aYiNPf~~~~~~g~~w~C~ 114 (140)
.+.++||+|||+||.+++++++++||||++|+||++.. ++|+++ .+|+||++|+|||||||+|++++++|+||
T Consensus 7 e~~~gvR~s~n~~P~t~~~~~~~~iPlg~v~tPl~~~~----~vp~v~---~~pvRC~~CraylNPf~~~d~~~~~W~C~ 79 (761)
T PLN00162 7 EAIDGVRMSWNVWPSSKIEASKCVIPLAALYTPLKPLP----ELPVLP---YDPLRCRTCRAVLNPYCRVDFQAKIWICP 79 (761)
T ss_pred cccCceEeeeecCCCCHHHHhcCCCCeEEEEecCCcCC----CCCcCC---CCCCccCCCcCEECCceEEecCCCEEEcc
Confidence 46689999999999999999999999999999998763 488887 57999999999999999999999999999
Q ss_pred cCCCCCCCCCCCc
Q 032449 115 FCGVWMLMRGLSS 127 (140)
Q Consensus 115 lC~~~N~lp~~~~ 127 (140)
||+..|.+|..+.
T Consensus 80 ~C~~~N~~P~~Y~ 92 (761)
T PLN00162 80 FCFQRNHFPPHYS 92 (761)
T ss_pred CCCCCCCCchHhc
Confidence 9999999997654
No 5
>PTZ00395 Sec24-related protein; Provisional
Probab=99.90 E-value=6e-25 Score=206.35 Aligned_cols=125 Identities=30% Similarity=0.457 Sum_probs=110.4
Q ss_pred CceEEeccCCCCCCCCCCCCceeEecccCCCCCCeeEeeccccCCCHHHHhhcCCCeEEEEeeccCCCCCCCCCceeccC
Q 032449 5 SVILYETRQGKSVKPPPPVTSKYIVKDTGNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFG 84 (140)
Q Consensus 5 ~~~~~~t~~~~~~~~pp~~~~~~~~~d~gn~~p~~vR~T~~~iP~t~~l~~~~~iPlgivv~Pf~~~~~~e~~vp~v~~~ 84 (140)
...+|+|++.. .||+.+++|+++|+|||+|+|||+|||.||.+.++++.+.|||||||+||+...++| .||.++..
T Consensus 623 ~~~~~~t~k~~---~pp~~~~~~~~~dtgn~dP~~~r~tmY~iP~~~~~~~~~~iP~gi~v~Pfa~~~~~e-~~~~~~~~ 698 (1560)
T PTZ00395 623 NLKVFETCKYI---SPPSYYQPYISIDTGKADPRFLKSTLYQIPLFSETLKLSQIPFGIIVNPFACLNEGE-GIDKIDMK 698 (1560)
T ss_pred cchhhhhccCC---CCCCCCCceEEeecCCCChhhhhhhhhcCcchHHHHHhcCCCceeecchhhhcCCCC-CCcccchh
Confidence 34789999887 589999999999999999999999999999999999999999999999999988776 58888765
Q ss_pred --------CCCeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCC-CCCcccccccc
Q 032449 85 --------ESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMR-GLSSVEGQLNL 134 (140)
Q Consensus 85 --------~~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp-~~~~~~~~~~~ 134 (140)
...|+||.+|++|+|+++.++.. +++.|+||+..+.+. +...+.-||+.
T Consensus 699 ~~~~d~~~~~~~~rc~~c~~y~~~~~~~~~~-~~~~c~~c~~~~~i~e~~~~~~~~~~~ 756 (1560)
T PTZ00395 699 DIINDKEENIEILRCPKCLGYLHATILEDIS-SSVQCVFCDTDFLINENVLFDIFQYNE 756 (1560)
T ss_pred hcccchhhccceeecchhHhhhcchheeccc-ceEEEEecCCcchhhHHHHHHHHHHhh
Confidence 24789999999999999999875 899999999999984 46666666654
No 6
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.79 E-value=2.7e-20 Score=166.59 Aligned_cols=97 Identities=22% Similarity=0.261 Sum_probs=87.0
Q ss_pred CCCCCCeeEeeccccCCCHHHHhhcCCCeEEEEeeccCCCCCCCCCceeccCCCCeeecCCCCcEEcCceeEEeCCcEEE
Q 032449 33 GNCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKSFV 112 (140)
Q Consensus 33 gn~~p~~vR~T~~~iP~t~~l~~~~~iPlgivv~Pf~~~~~~e~~vp~v~~~~~~~~RC~~C~aYiNPf~~~~~~g~~w~ 112 (140)
.+.+.+.||+|||+||.++....++.+|++++++||.+.. .+|.+. ++|+||++|+||+||||.+|.+.+.|+
T Consensus 5 ~~e~~dGvR~twnvwPs~~~~~~~~vvPla~lytPl~e~~----~~~~~~---y~P~~C~~C~AvlNPyc~vd~~a~~W~ 77 (745)
T KOG1986|consen 5 DIEEIDGVRFTWNVWPSTRAEASRTVVPLACLYTPLKERP----DLPPIQ---YDPLRCSKCGAVLNPYCSVDFRAKSWI 77 (745)
T ss_pred ccccCCCcccccccCCCcccccccccccHHHhccccccCC----CCCccC---CCCchhccchhhcCcceeecccCceEe
Confidence 3567899999999999999999999999999999998653 256664 789999999999999999999999999
Q ss_pred EccCCCCCCCCCCCcccccccccc
Q 032449 113 CNFCGVWMLMRGLSSVEGQLNLLL 136 (140)
Q Consensus 113 C~lC~~~N~lp~~~~~~~~~~~~~ 136 (140)
|+||.+.|.+|..|......++|.
T Consensus 78 CpfC~qrN~~p~~Y~~is~~n~P~ 101 (745)
T KOG1986|consen 78 CPFCNQRNPFPPHYSGISENNLPP 101 (745)
T ss_pred ccccccCCCCChhhcccCccCCCh
Confidence 999999999999888888877764
No 7
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=99.73 E-value=1.1e-18 Score=154.21 Aligned_cols=97 Identities=23% Similarity=0.335 Sum_probs=87.8
Q ss_pred CCCCCeeEeeccccCCCHHHHhhcCCCeEEEEeeccCCCCCCCCCceeccCCCCeeecCC-CCcEEcCceeEEeCCcEEE
Q 032449 34 NCSPRYIRCSLNQIPCTENLLKLSSMPSALMVQVLALPDPSEDPIPVVDFGESGLVRCCC-CRGYRNPFMEFVDNGKSFV 112 (140)
Q Consensus 34 n~~p~~vR~T~~~iP~t~~l~~~~~iPlgivv~Pf~~~~~~e~~vp~v~~~~~~~~RC~~-C~aYiNPf~~~~~~g~~w~ 112 (140)
+.+.++||+|||+||.++....++.+|++++++||.+.+ .+++. .+.|+.|.. |+||+||||.++.+.+.|+
T Consensus 6 iee~dgir~twnvfpat~~da~~~~iPia~lY~Pl~e~~----~~~v~---~yepv~C~~pC~avlnpyC~id~r~~~W~ 78 (755)
T COG5047 6 IEENDGIRLTWNVFPATRGDATRTVIPIACLYTPLHEDD----ALTVN---YYEPVKCTAPCKAVLNPYCHIDERNQSWI 78 (755)
T ss_pred hccccceEEEEecccCCccccccccccHHHhcccccccc----ccCcc---cCCCceecccchhhcCcceeeccCCceEe
Confidence 467889999999999999999999999999999998653 24444 378999999 9999999999999999999
Q ss_pred EccCCCCCCCCCCCccccccccccC
Q 032449 113 CNFCGVWMLMRGLSSVEGQLNLLLQ 137 (140)
Q Consensus 113 C~lC~~~N~lp~~~~~~~~~~~~~~ 137 (140)
|+||+..|.||..+.+.++.+|||.
T Consensus 79 CpfCnqrn~lp~qy~~iS~~~Lple 103 (755)
T COG5047 79 CPFCNQRNTLPPQYRDISNANLPLE 103 (755)
T ss_pred cceecCCCCCChhhcCCCcccCCcc
Confidence 9999999999999999999999874
No 8
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=99.73 E-value=5.4e-19 Score=106.77 Aligned_cols=39 Identities=49% Similarity=1.016 Sum_probs=27.7
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMRGL 125 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp~~ 125 (140)
+|+||++|+||||||++|++++++|+|+||++.|.||..
T Consensus 1 ~p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp~~ 39 (40)
T PF04810_consen 1 GPVRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLPPH 39 (40)
T ss_dssp -S-B-TTT--BS-TTSEEETTTTEEEETTT--EEE--GG
T ss_pred CccccCCCCCEECCcceEcCCCCEEECcCCCCcCCCCCC
Confidence 489999999999999999999999999999999999864
No 9
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.31 E-value=0.11 Score=34.04 Aligned_cols=32 Identities=34% Similarity=0.827 Sum_probs=22.8
Q ss_pred CceeccCCCCeeecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 78 IPVVDFGESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 78 vp~v~~~~~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
.|--+.|+..|.||++||-. |..|+|+-||..
T Consensus 28 F~CPnCGe~~I~Rc~~CRk~----------g~~Y~Cp~CGF~ 59 (61)
T COG2888 28 FPCPNCGEVEIYRCAKCRKL----------GNPYRCPKCGFE 59 (61)
T ss_pred eeCCCCCceeeehhhhHHHc----------CCceECCCcCcc
Confidence 33446677789999999853 456778888764
No 10
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=89.19 E-value=0.35 Score=27.49 Aligned_cols=29 Identities=28% Similarity=0.445 Sum_probs=22.5
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCCCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWML 121 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~ 121 (140)
+.|..|++-|-- -.+..+++|.+|...|.
T Consensus 2 ~~C~~C~t~L~y----P~gA~~vrCs~C~~vt~ 30 (31)
T TIGR01053 2 VVCGGCRTLLMY----PRGASSVRCALCQTVNL 30 (31)
T ss_pred cCcCCCCcEeec----CCCCCeEECCCCCeEec
Confidence 578899988752 25678999999998774
No 11
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.48 E-value=0.31 Score=28.43 Aligned_cols=33 Identities=21% Similarity=0.516 Sum_probs=24.0
Q ss_pred eeecCCCCcEEc-CceeEEeCCcEEEEccCCCCC
Q 032449 88 LVRCCCCRGYRN-PFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 88 ~~RC~~C~aYiN-Pf~~~~~~g~~w~C~lC~~~N 120 (140)
+++|.+|++-.+ |--++...|++.+|.-|++.-
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 478888887766 555566677888888888753
No 12
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=88.22 E-value=0.37 Score=30.68 Aligned_cols=34 Identities=15% Similarity=0.260 Sum_probs=24.7
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
-.+-|++|++-=.-+-+-+...-+|+|..|+..|
T Consensus 21 ~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 21 YALICSKCFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred eeEECcccchhhcccccccCCceEEEcCCCCCcC
Confidence 3567999987644332555555699999999987
No 13
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=87.83 E-value=0.37 Score=32.26 Aligned_cols=30 Identities=27% Similarity=0.635 Sum_probs=20.8
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMR 123 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp 123 (140)
|.|| +|+.|+ ..+++.++-+| .||....+.
T Consensus 3 ifrC-~Cgr~l----ya~e~~kTkkC-~CG~~l~vk 32 (68)
T PF09082_consen 3 IFRC-DCGRYL----YAKEGAKTKKC-VCGKTLKVK 32 (68)
T ss_dssp EEEE-TTS--E----EEETT-SEEEE-TTTEEEE--
T ss_pred EEEe-cCCCEE----EecCCcceeEe-cCCCeeeee
Confidence 7899 799986 35677789999 999888775
No 14
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.69 E-value=0.63 Score=28.11 Aligned_cols=31 Identities=23% Similarity=0.636 Sum_probs=21.7
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLM 122 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~l 122 (140)
..+|.+|++-+- ++.....++|+.||....+
T Consensus 3 ~y~C~~CG~~~~----~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 3 EYKCARCGREVE----LDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EEECCCCCCEEE----ECCCCCceECCCCCCeEEE
Confidence 468999999553 3333347999999976543
No 15
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=83.86 E-value=0.5 Score=30.82 Aligned_cols=28 Identities=32% Similarity=0.701 Sum_probs=19.4
Q ss_pred ccCCCCeeecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 82 DFGESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 82 ~~~~~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
+.|+..|.||.+||-.- ..|+|+-||..
T Consensus 30 nCG~~~I~RC~~CRk~~----------~~Y~CP~CGF~ 57 (59)
T PRK14890 30 NCGEVIIYRCEKCRKQS----------NPYTCPKCGFE 57 (59)
T ss_pred CCCCeeEeechhHHhcC----------CceECCCCCCc
Confidence 34555588999998544 45678888764
No 16
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=83.11 E-value=0.74 Score=27.96 Aligned_cols=32 Identities=25% Similarity=0.399 Sum_probs=21.7
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMR 123 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp 123 (140)
-|.+|+..|-+- -..++..|.|+-|+....+.
T Consensus 2 FCp~Cg~~l~~~--~~~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPK--EGKEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCccccc--cCCCCCEEECCcCCCeEECC
Confidence 488898877332 22223589999999877664
No 17
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=80.16 E-value=1.3 Score=32.01 Aligned_cols=32 Identities=13% Similarity=0.236 Sum_probs=26.1
Q ss_pred eeecCCCCcEEcCceeEEe-CCcEEEEccCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVD-NGKSFVCNFCGVW 119 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~-~g~~w~C~lC~~~ 119 (140)
-..|..|+-.|..-|.+.. +...|.|.+|...
T Consensus 71 ~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC~k~ 103 (118)
T PF02318_consen 71 GRVCVDCKHRVCKKCGVYSKKEPIWLCKVCQKQ 103 (118)
T ss_dssp CEEETTTTEEEETTSEEETSSSCCEEEHHHHHH
T ss_pred CCcCCcCCccccCccCCcCCCCCCEEChhhHHH
Confidence 3889999999998888874 5679999999643
No 18
>PRK03954 ribonuclease P protein component 4; Validated
Probab=79.06 E-value=1.4 Score=32.61 Aligned_cols=37 Identities=22% Similarity=0.354 Sum_probs=25.8
Q ss_pred eecCCCCcEEcCc----eeEEeCC---cEEEEccCCCCCCCCCC
Q 032449 89 VRCCCCRGYRNPF----MEFVDNG---KSFVCNFCGVWMLMRGL 125 (140)
Q Consensus 89 ~RC~~C~aYiNPf----~~~~~~g---~~w~C~lC~~~N~lp~~ 125 (140)
--|++|.+||=|- +.+..+. -.++|..||+..-+|-.
T Consensus 65 ~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~P~~ 108 (121)
T PRK03954 65 RYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRYPYL 108 (121)
T ss_pred HHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEeeccc
Confidence 4599999999773 3343321 23599999999887743
No 19
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=78.02 E-value=1.4 Score=25.57 Aligned_cols=32 Identities=19% Similarity=0.482 Sum_probs=20.2
Q ss_pred eeecCCCCcEEc-CceeEEeCCcEEEEccCCCC
Q 032449 88 LVRCCCCRGYRN-PFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 88 ~~RC~~C~aYiN-Pf~~~~~~g~~w~C~lC~~~ 119 (140)
.++|.+|++-.+ +=-++-..|++.+|.-|++.
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 467777776554 33334456677777777764
No 20
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=75.81 E-value=1.3 Score=26.36 Aligned_cols=30 Identities=20% Similarity=0.389 Sum_probs=25.4
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
-||.+|+....=+..+.+ .....|+-|+..
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISE-DDPVPCPECGST 35 (42)
T ss_pred EEeCCCCCEEEEEEEcCC-CCCCcCCCCCCC
Confidence 689999988888887777 678999999973
No 21
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=73.97 E-value=2 Score=34.97 Aligned_cols=51 Identities=16% Similarity=0.068 Sum_probs=35.9
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCC---CCCccccccccccCc
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMR---GLSSVEGQLNLLLQG 138 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp---~~~~~~~~~~~~~~~ 138 (140)
-+-|++|.-==+-+---...-..|+|.+|++.|..+ ..+++..|++-+-||
T Consensus 192 alIC~~C~hhngl~~~~ek~~~efiC~~Cn~~n~~~~~~~dsn~~~~p~~~s~~ 245 (251)
T COG5415 192 ALICPQCHHHNGLYRLAEKPIIEFICPHCNHKNDEVKEREDSNEAKQPAQPSQS 245 (251)
T ss_pred hhccccccccccccccccccchheecccchhhcCcccccccchhhcCCCCcccc
Confidence 366777765444333333444579999999999876 477788888887776
No 22
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=73.71 E-value=3.9 Score=24.20 Aligned_cols=27 Identities=26% Similarity=0.639 Sum_probs=19.8
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
+|..|++-- ..+|.....++|.-||..
T Consensus 2 ~Cp~Cg~~~---~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE---IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE---EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc---eEEcCCCCeEECCCCCCE
Confidence 688888833 467777788999999854
No 23
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=73.34 E-value=2.3 Score=30.63 Aligned_cols=28 Identities=14% Similarity=0.214 Sum_probs=19.9
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
...||..|+.... .....|.|+-||..+
T Consensus 69 ~~~~C~~Cg~~~~------~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 69 AQAWCWDCSQVVE------IHQHDAQCPHCHGER 96 (113)
T ss_pred cEEEcccCCCEEe------cCCcCccCcCCCCCC
Confidence 4689999995433 323567899999654
No 24
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=73.33 E-value=2.2 Score=24.09 Aligned_cols=24 Identities=25% Similarity=0.501 Sum_probs=15.6
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
+|..|+=...+-. .-|.|++|+..
T Consensus 3 ~C~~CGy~y~~~~------~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGEE------APWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCCc------CCCcCcCCCCc
Confidence 6777774333322 57999999873
No 25
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=72.23 E-value=1.9 Score=26.27 Aligned_cols=31 Identities=23% Similarity=0.396 Sum_probs=22.7
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
-||.+|+....-+..+.+ .....|+.|+..+
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~~~ 36 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSD-DPLATCPECGGEK 36 (52)
T ss_pred EEeCCCCCEeEEEEecCC-CCCCCCCCCCCCc
Confidence 589999986666555544 3567899999854
No 26
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=72.12 E-value=2.6 Score=30.39 Aligned_cols=28 Identities=21% Similarity=0.282 Sum_probs=20.5
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
...||.+|+.+..+- ...|.|+-|+..+
T Consensus 69 ~~~~C~~Cg~~~~~~------~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 69 VECECEDCSEEVSPE------IDLYRCPKCHGIM 96 (115)
T ss_pred cEEEcccCCCEEecC------CcCccCcCCcCCC
Confidence 458999999655432 2368999999765
No 27
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=71.85 E-value=3 Score=24.30 Aligned_cols=27 Identities=22% Similarity=0.460 Sum_probs=20.7
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
..+|..|++. +...++ .+|.|.-||+.
T Consensus 8 ~~~C~~C~~~---~~~~~d--G~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSR---WFYSDD--GFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCe---EeEccC--CEEEhhhCceE
Confidence 3679999999 554544 38999999975
No 28
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=71.67 E-value=1.5 Score=27.79 Aligned_cols=36 Identities=22% Similarity=0.411 Sum_probs=25.1
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCCCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMRGLS 126 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp~~~ 126 (140)
+||.+|+-.|----.+.. -.-+|+=|++.|.+....
T Consensus 5 iRC~~CnklLa~~g~~~~--leIKCpRC~tiN~~~a~~ 40 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIE--LEIKCPRCKTINHVRATS 40 (51)
T ss_pred eeccchhHHHhhhcCccE--EEEECCCCCccceEeccC
Confidence 899999876654211221 258999999999987644
No 29
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=70.92 E-value=1.6 Score=27.29 Aligned_cols=30 Identities=30% Similarity=0.635 Sum_probs=19.4
Q ss_pred ecCCCCcEEcCc-----------eeEEeCCcEEEEccCCCC
Q 032449 90 RCCCCRGYRNPF-----------MEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 90 RC~~C~aYiNPf-----------~~~~~~g~~w~C~lC~~~ 119 (140)
+|..|+-..+|- +.|++--..|+|++|+..
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 677777555543 334444457999999853
No 30
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=69.22 E-value=7.1 Score=22.29 Aligned_cols=30 Identities=30% Similarity=0.609 Sum_probs=21.1
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
.+.+|..|++-+ -+........|.+|+...
T Consensus 2 ~~~~C~~C~~~~----i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 2 NLKKCSKCGGNG----IVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred CceEcCCCCCCe----EEEecCCeEEcccCCcEe
Confidence 367899999866 221333589999999764
No 31
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=69.20 E-value=3.1 Score=30.73 Aligned_cols=34 Identities=15% Similarity=0.457 Sum_probs=23.0
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMRG 124 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp~ 124 (140)
++|.-|+..- -..++...+.|.|.-|+..|.+..
T Consensus 1 v~C~fC~~~s--~~~~~~~~~~w~C~~C~q~N~f~e 34 (131)
T PF09779_consen 1 VNCWFCGQNS--KVPYDNRNSNWTCPHCEQYNGFDE 34 (131)
T ss_pred CeeccCCCCC--CCCCCCCCCeeECCCCCCccCccc
Confidence 3677776653 233344455699999999997754
No 32
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=68.66 E-value=3.5 Score=29.71 Aligned_cols=29 Identities=21% Similarity=0.369 Sum_probs=19.4
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
...||.+|+.+...- ....|.|+-||..+
T Consensus 69 ~~~~C~~Cg~~~~~~-----~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 69 AECWCETCQQYVTLL-----TQRVRRCPQCHGDM 97 (114)
T ss_pred cEEEcccCCCeeecC-----CccCCcCcCcCCCC
Confidence 458999999643221 11248899999664
No 33
>PRK12722 transcriptional activator FlhC; Provisional
Probab=68.64 E-value=2.2 Score=33.71 Aligned_cols=31 Identities=35% Similarity=0.740 Sum_probs=22.0
Q ss_pred CCCeeecCCCCc-EEcCceeEEeCCcEEEEccCCC
Q 032449 85 ESGLVRCCCCRG-YRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 85 ~~~~~RC~~C~a-YiNPf~~~~~~g~~w~C~lC~~ 118 (140)
...+.+|++|++ ||-.. .+....++|++|.-
T Consensus 131 ~L~l~~C~~Cgg~fv~~~---~e~~~~f~CplC~~ 162 (187)
T PRK12722 131 MLQLSSCNCCGGHFVTHA---HDPVGSFVCGLCQP 162 (187)
T ss_pred cEeeccCCCCCCCeeccc---cccCCCCcCCCCCC
Confidence 355789999986 55222 24457899999985
No 34
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=68.50 E-value=2.5 Score=24.26 Aligned_cols=29 Identities=24% Similarity=0.409 Sum_probs=21.6
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
.||..|+..+.-...+.+ +....|+-|+.
T Consensus 6 y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 6 YRCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 589999987766655544 56788999987
No 35
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=66.05 E-value=3.7 Score=32.53 Aligned_cols=27 Identities=30% Similarity=0.591 Sum_probs=21.8
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
-.||++|++-|=. .++..+|+-|+..-
T Consensus 149 ~A~CsrC~~~L~~------~~~~l~Cp~Cg~tE 175 (188)
T COG1096 149 YARCSRCRAPLVK------KGNMLKCPNCGNTE 175 (188)
T ss_pred EEEccCCCcceEE------cCcEEECCCCCCEE
Confidence 4799999998743 56899999999753
No 36
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=64.09 E-value=2.2 Score=24.64 Aligned_cols=29 Identities=28% Similarity=0.534 Sum_probs=13.7
Q ss_pred cCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 91 C~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
|..|++=+.--.--.++..+++|.-|+..
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred cccccChhhhhcCCCCCccceECCCCCCE
Confidence 66777665433222256678888888754
No 37
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=62.85 E-value=4.2 Score=25.52 Aligned_cols=31 Identities=23% Similarity=0.626 Sum_probs=21.7
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLM 122 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~l 122 (140)
.=+|.+|++-+ ..+.......|+-||+.-.+
T Consensus 6 ~Y~C~~Cg~~~----~~~~~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 6 EYKCARCGREV----ELDQETRGIRCPYCGSRILV 36 (49)
T ss_pred EEEhhhcCCee----ehhhccCceeCCCCCcEEEE
Confidence 45788888877 44555677888888876433
No 38
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=62.82 E-value=5.3 Score=25.57 Aligned_cols=29 Identities=28% Similarity=0.573 Sum_probs=22.3
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
--.|..|+...-- ...++.|.|.-||..-
T Consensus 28 Sq~C~~CG~~~~~----~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKK----RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCccccccc----ccccceEEcCCCCCEE
Confidence 3568888877665 4567899999999863
No 39
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=61.53 E-value=7.3 Score=20.91 Aligned_cols=24 Identities=29% Similarity=0.667 Sum_probs=16.2
Q ss_pred cCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 91 C~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
|.+|+.-|-|-- .+..|.|+-||.
T Consensus 1 C~sC~~~i~~r~----~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPRE----QAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcc----cCceEeCCCCCC
Confidence 667777777653 245788888873
No 40
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=60.96 E-value=3.7 Score=21.54 Aligned_cols=21 Identities=29% Similarity=0.627 Sum_probs=12.4
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
+|.+|++-|..-.+| |+-||+
T Consensus 1 ~Cp~CG~~~~~~~~f--------C~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKF--------CPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcc--------hhhhCC
Confidence 467777766543333 666665
No 41
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=60.77 E-value=7.7 Score=21.15 Aligned_cols=29 Identities=28% Similarity=0.544 Sum_probs=16.4
Q ss_pred ecCCCCcEEcCc-eeEEeCCcE-----EEEccCCC
Q 032449 90 RCCCCRGYRNPF-MEFVDNGKS-----FVCNFCGV 118 (140)
Q Consensus 90 RC~~C~aYiNPf-~~~~~~g~~-----w~C~lC~~ 118 (140)
||.+|+-.|-+- ..+...++. |.|..|+.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~ 35 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGK 35 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCC
Confidence 678888877763 223333333 35666654
No 42
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=59.63 E-value=11 Score=22.58 Aligned_cols=27 Identities=15% Similarity=0.472 Sum_probs=19.2
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
+.|.+|++- ..| .......|.|.-|++
T Consensus 19 ~~CP~Cg~~-~~~--~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-KHY--RLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-eeE--EeCCCCeEECCCCCC
Confidence 669999987 332 223357999999985
No 43
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=58.99 E-value=3.1 Score=22.72 Aligned_cols=13 Identities=15% Similarity=0.373 Sum_probs=11.3
Q ss_pred EEEEccCCCCCCC
Q 032449 110 SFVCNFCGVWMLM 122 (140)
Q Consensus 110 ~w~C~lC~~~N~l 122 (140)
.|.|..|...|..
T Consensus 4 ~W~C~~C~~~N~~ 16 (30)
T PF00641_consen 4 DWKCPSCTFMNPA 16 (30)
T ss_dssp SEEETTTTEEEES
T ss_pred CccCCCCcCCchH
Confidence 7999999999854
No 44
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=58.86 E-value=4.2 Score=29.43 Aligned_cols=29 Identities=21% Similarity=0.198 Sum_probs=18.8
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
...||.+|+.+..+- . ...+.|+-|+..+
T Consensus 70 ~~~~C~~Cg~~~~~~----~-~~~~~CP~Cgs~~ 98 (117)
T PRK00564 70 VELECKDCSHVFKPN----A-LDYGVCEKCHSKN 98 (117)
T ss_pred CEEEhhhCCCccccC----C-ccCCcCcCCCCCc
Confidence 469999999543321 1 1234599999765
No 45
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=58.60 E-value=16 Score=27.22 Aligned_cols=33 Identities=27% Similarity=0.602 Sum_probs=26.8
Q ss_pred eeecCCCCcEEcCceeEEeCCcEE--EEccCCCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSF--VCNFCGVWMLMR 123 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w--~C~lC~~~N~lp 123 (140)
-+-|+.|+. |=..+...++.| .|..||..-.+.
T Consensus 97 yVlC~~C~s---PdT~l~k~~r~~~l~C~ACGa~~~v~ 131 (133)
T TIGR00311 97 YVICRECNR---PDTRIIKEGRVSLLKCEACGAKAPLR 131 (133)
T ss_pred eEECCCCCC---CCcEEEEeCCeEEEecccCCCCCccC
Confidence 488999995 888888877776 899999987653
No 46
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=57.54 E-value=8.1 Score=28.72 Aligned_cols=33 Identities=24% Similarity=0.514 Sum_probs=22.7
Q ss_pred eeecCCCCcEEcCce-----------eEEeCCcEEEEccCCCCC
Q 032449 88 LVRCCCCRGYRNPFM-----------EFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~-----------~~~~~g~~w~C~lC~~~N 120 (140)
..||..|.+=+-+-- .+......|+|+-|++..
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 589999999654321 222345699999999754
No 47
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=57.51 E-value=11 Score=20.46 Aligned_cols=24 Identities=25% Similarity=0.588 Sum_probs=12.3
Q ss_pred cCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 91 C~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
|.+||+.|- .-.+...++|..|.+
T Consensus 1 C~~Cr~~L~----yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLM----YPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEE----cCCCCCCeECCccCc
Confidence 445555543 113445666666654
No 48
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=56.10 E-value=7.6 Score=26.93 Aligned_cols=27 Identities=26% Similarity=0.471 Sum_probs=20.5
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCCCCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLM 122 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~l 122 (140)
-|.+|++.|.|- +..+.|..|+.....
T Consensus 2 fC~~Cg~~l~~~------~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPK------NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccC------CCeEECcCCCCcccc
Confidence 488999999652 247999999976544
No 49
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=55.72 E-value=0.86 Score=28.29 Aligned_cols=32 Identities=22% Similarity=0.439 Sum_probs=13.0
Q ss_pred CeeecCCCCcEE----cCceeEEeCCcEEEEccCCC
Q 032449 87 GLVRCCCCRGYR----NPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 87 ~~~RC~~C~aYi----NPf~~~~~~g~~w~C~lC~~ 118 (140)
.|+|=..|.=.- .-|.+.......|.|++|++
T Consensus 14 ~P~Rg~~C~H~~CFDl~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 14 IPVRGKNCKHLQCFDLESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp SEEEETT--SS--EEHHHHHHHHHHS---B-TTT--
T ss_pred eCccCCcCcccceECHHHHHHHhhccCCeECcCCcC
Confidence 355555555432 13444445567899999986
No 50
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=55.61 E-value=3.1 Score=25.71 Aligned_cols=30 Identities=30% Similarity=0.616 Sum_probs=14.7
Q ss_pred ecCCCCcEEcCc-----------eeEEeCCcEEEEccCCCC
Q 032449 90 RCCCCRGYRNPF-----------MEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 90 RC~~C~aYiNPf-----------~~~~~~g~~w~C~lC~~~ 119 (140)
+|..|+-.-+|- ..|++--..|+|+.|+..
T Consensus 3 ~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 3 QCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred CCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 566676444432 223333456999999864
No 51
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=54.75 E-value=9.8 Score=21.59 Aligned_cols=31 Identities=23% Similarity=0.447 Sum_probs=13.9
Q ss_pred eecCCCCcEEc-CceeEEeCCcEEEEccCCCC
Q 032449 89 VRCCCCRGYRN-PFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 89 ~RC~~C~aYiN-Pf~~~~~~g~~w~C~lC~~~ 119 (140)
++|.+|++-.- +=-.+...+.+..|+-|++.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 45666665321 11112223345666666653
No 52
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=54.58 E-value=7.4 Score=33.78 Aligned_cols=36 Identities=19% Similarity=0.579 Sum_probs=26.1
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCCCCCccc
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMRGLSSVE 129 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp~~~~~~ 129 (140)
...-||.+|+ |.-..-.|-|+-|+..-.+..+-.+.
T Consensus 352 ~~~YRC~~CG--------F~a~~l~W~CPsC~~W~TikPir~~~ 387 (389)
T COG2956 352 KPRYRCQNCG--------FTAHTLYWHCPSCRAWETIKPIRGLD 387 (389)
T ss_pred cCCceecccC--------CcceeeeeeCCCcccccccCCccccc
Confidence 4568999997 33344589999999988776554443
No 53
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=53.47 E-value=6.9 Score=19.03 Aligned_cols=10 Identities=40% Similarity=1.059 Sum_probs=6.4
Q ss_pred EEEccCCCCC
Q 032449 111 FVCNFCGVWM 120 (140)
Q Consensus 111 w~C~lC~~~N 120 (140)
|+|.+|+...
T Consensus 1 ~~C~~C~~~~ 10 (24)
T PF13894_consen 1 FQCPICGKSF 10 (24)
T ss_dssp EE-SSTS-EE
T ss_pred CCCcCCCCcC
Confidence 7899998754
No 54
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=53.46 E-value=8.8 Score=23.26 Aligned_cols=32 Identities=22% Similarity=0.331 Sum_probs=23.3
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
.+.++|..|+.-|...-.- .....|.|.-...
T Consensus 3 ~g~l~C~~CG~~m~~~~~~-~~~~yy~C~~~~~ 34 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRKRK-GKYRYYRCSNRRR 34 (58)
T ss_pred CCcEEcccCCcEeEEEECC-CCceEEEcCCCcC
Confidence 3579999999998875432 3447899986653
No 55
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=52.57 E-value=7.5 Score=24.19 Aligned_cols=25 Identities=20% Similarity=0.554 Sum_probs=18.3
Q ss_pred eecCCCCc-EEcCceeEEeCCcEEEEccCCCC
Q 032449 89 VRCCCCRG-YRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 89 ~RC~~C~a-YiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
.-|.+|++ +|-+.- .+|.|.-|+..
T Consensus 21 ~fCP~Cg~~~m~~~~------~r~~C~~Cgyt 46 (50)
T PRK00432 21 KFCPRCGSGFMAEHL------DRWHCGKCGYT 46 (50)
T ss_pred CcCcCCCcchheccC------CcEECCCcCCE
Confidence 47999998 554432 58999999864
No 56
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.45 E-value=7.8 Score=30.92 Aligned_cols=24 Identities=33% Similarity=0.779 Sum_probs=19.1
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
-..|..|+. ..++.|.|+-||...
T Consensus 309 S~~C~~cg~---------~~~r~~~C~~cg~~~ 332 (364)
T COG0675 309 SKTCPCCGH---------LSGRLFKCPRCGFVH 332 (364)
T ss_pred cccccccCC---------ccceeEECCCCCCee
Confidence 378999988 336799999999854
No 57
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=52.33 E-value=9.7 Score=25.15 Aligned_cols=31 Identities=23% Similarity=0.358 Sum_probs=16.6
Q ss_pred eeecCCCCcEEcCc----eeEE-----eCCcEEEEccCCC
Q 032449 88 LVRCCCCRGYRNPF----MEFV-----DNGKSFVCNFCGV 118 (140)
Q Consensus 88 ~~RC~~C~aYiNPf----~~~~-----~~g~~w~C~lC~~ 118 (140)
-.-|++|++++=|- .++. ...-.|+|..|++
T Consensus 46 r~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 46 RTICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp CTB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred cccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 45799999998874 3333 2334688999974
No 58
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=52.18 E-value=7.5 Score=22.17 Aligned_cols=11 Identities=36% Similarity=0.926 Sum_probs=9.4
Q ss_pred EEEEccCCCCC
Q 032449 110 SFVCNFCGVWM 120 (140)
Q Consensus 110 ~w~C~lC~~~N 120 (140)
.|+|..||.+-
T Consensus 2 ~~~C~~CG~i~ 12 (34)
T cd00729 2 VWVCPVCGYIH 12 (34)
T ss_pred eEECCCCCCEe
Confidence 69999999774
No 59
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=51.64 E-value=7.4 Score=24.22 Aligned_cols=32 Identities=25% Similarity=0.609 Sum_probs=25.6
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
+.+|.+|++=-.|.-.-...|....||.|+..
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~ 34 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLY 34 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHH
Confidence 46899999888887766666777999999843
No 60
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=51.08 E-value=8.4 Score=29.90 Aligned_cols=14 Identities=43% Similarity=0.942 Sum_probs=9.6
Q ss_pred CCcEEEEccCCCCC
Q 032449 107 NGKSFVCNFCGVWM 120 (140)
Q Consensus 107 ~g~~w~C~lC~~~N 120 (140)
+|+.|+|..||..-
T Consensus 131 ~~~~~vC~vCGy~~ 144 (166)
T COG1592 131 EGKVWVCPVCGYTH 144 (166)
T ss_pred cCCEEEcCCCCCcc
Confidence 34578888887654
No 61
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=51.04 E-value=2.3 Score=24.67 Aligned_cols=32 Identities=22% Similarity=0.430 Sum_probs=14.4
Q ss_pred CCeeecCCCCcEEcCceeE---EeCCcEEEEccCC
Q 032449 86 SGLVRCCCCRGYRNPFMEF---VDNGKSFVCNFCG 117 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~---~~~g~~w~C~lC~ 117 (140)
..+++|++|.-.+.-.|.- ...+..|.|..|.
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--SS-----HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCCCCcEECCcCC
Confidence 3579999999999954421 1234469998773
No 62
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=50.05 E-value=9 Score=20.84 Aligned_cols=27 Identities=19% Similarity=0.567 Sum_probs=14.9
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
.|.+|+.++-.... .+...+.|+-|..
T Consensus 3 ~C~rC~~~~~~~~~--~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGI--NGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEE--TTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEe--cCCCCeECcCCcC
Confidence 58999998654432 3445789988864
No 63
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=49.62 E-value=12 Score=31.98 Aligned_cols=36 Identities=14% Similarity=0.219 Sum_probs=23.8
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMR 123 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp 123 (140)
-+-|++|+.==+-.-+-+..--.|+|..|++.|.=+
T Consensus 220 ALIC~~C~~HNGla~~ee~~yi~F~C~~Cn~LN~~~ 255 (328)
T KOG2846|consen 220 ALICSQCHHHNGLARKEEYEYITFRCPHCNALNPAK 255 (328)
T ss_pred hhcchhhccccCcCChhhcCceEEECccccccCCCc
Confidence 367898886544333222333589999999999654
No 64
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=49.26 E-value=16 Score=22.13 Aligned_cols=25 Identities=20% Similarity=0.360 Sum_probs=11.8
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
+|.+|++-+..- .+..-+|+-||+.
T Consensus 4 ~C~~Cg~~~~~~-----~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIK-----SKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecC-----CCCceECCCCCce
Confidence 455555543321 2344555555543
No 65
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=49.08 E-value=8.7 Score=33.86 Aligned_cols=30 Identities=17% Similarity=0.318 Sum_probs=23.4
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMRG 124 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp~ 124 (140)
..-+|++|+ +....+.|+|+-|+..|.+..
T Consensus 6 ~~y~C~~Cg--------~~~~~~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 6 SKFVCQHCG--------ADSPKWQGKCPACHAWNTITE 35 (454)
T ss_pred CeEECCcCC--------CCCccccEECcCCCCccccch
Confidence 346777776 455667899999999998866
No 66
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.37 E-value=12 Score=27.74 Aligned_cols=34 Identities=18% Similarity=0.375 Sum_probs=20.9
Q ss_pred CeeecCCCCcEEcCce-e------------EEe--CCcEEEEccCCCCC
Q 032449 87 GLVRCCCCRGYRNPFM-E------------FVD--NGKSFVCNFCGVWM 120 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~-~------------~~~--~g~~w~C~lC~~~N 120 (140)
...||..|+.....-- + +.. ....+.|+-||..+
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 4689999996544320 0 000 03568899999764
No 67
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=48.18 E-value=7.1 Score=20.35 Aligned_cols=13 Identities=15% Similarity=0.498 Sum_probs=11.0
Q ss_pred EEEEccCCCCCCC
Q 032449 110 SFVCNFCGVWMLM 122 (140)
Q Consensus 110 ~w~C~lC~~~N~l 122 (140)
.|+|..|...|.-
T Consensus 2 ~W~C~~C~~~N~~ 14 (26)
T smart00547 2 DWECPACTFLNFA 14 (26)
T ss_pred cccCCCCCCcChh
Confidence 5999999998854
No 68
>PF12773 DZR: Double zinc ribbon
Probab=48.12 E-value=7.1 Score=23.42 Aligned_cols=30 Identities=17% Similarity=0.223 Sum_probs=22.2
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWML 121 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~ 121 (140)
+-..|.+|++-|. ......++|.-|+..+.
T Consensus 11 ~~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 11 DAKFCPHCGTPLP-----PPDQSKKICPNCGAENP 40 (50)
T ss_pred cccCChhhcCChh-----hccCCCCCCcCCcCCCc
Confidence 3578888888887 34456788999988763
No 69
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.96 E-value=9.2 Score=27.92 Aligned_cols=33 Identities=18% Similarity=0.179 Sum_probs=19.7
Q ss_pred CeeecCCCCcEEcCc-eeEEeCCcEEEEccCCCCC
Q 032449 87 GLVRCCCCRGYRNPF-MEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf-~~~~~~g~~w~C~lC~~~N 120 (140)
...|| +|+.+...- ...+.-.-.|.|+-||..+
T Consensus 69 ~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~ 102 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKR 102 (124)
T ss_pred eeEEe-eCcCcccccccchhccccCCcCcCCCCCC
Confidence 45899 999775432 1111111137899999654
No 70
>PRK12860 transcriptional activator FlhC; Provisional
Probab=47.65 E-value=9.4 Score=30.25 Aligned_cols=30 Identities=37% Similarity=0.853 Sum_probs=21.9
Q ss_pred CCCeeecCCCCc-EEcCceeEEeCCcEEEEccCC
Q 032449 85 ESGLVRCCCCRG-YRNPFMEFVDNGKSFVCNFCG 117 (140)
Q Consensus 85 ~~~~~RC~~C~a-YiNPf~~~~~~g~~w~C~lC~ 117 (140)
...+.+|++|++ ||-. ..+....++|++|.
T Consensus 131 ~L~l~~C~~Cgg~fv~~---~~e~~~~f~CplC~ 161 (189)
T PRK12860 131 MLQLARCCRCGGKFVTH---AHDLRHNFVCGLCQ 161 (189)
T ss_pred CeeeccCCCCCCCeecc---ccccCCCCcCCCCC
Confidence 456899999986 5522 22556789999998
No 71
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=46.45 E-value=7 Score=30.43 Aligned_cols=31 Identities=35% Similarity=0.675 Sum_probs=12.6
Q ss_pred CCCeeecCCCCc-EEcCceeEEeCCcEEEEccCCC
Q 032449 85 ESGLVRCCCCRG-YRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 85 ~~~~~RC~~C~a-YiNPf~~~~~~g~~w~C~lC~~ 118 (140)
...+.+|.+|++ ||..- .+....++|++|+-
T Consensus 131 ~l~l~~C~~C~~~fv~~~---~~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 131 MLQLAPCRRCGGHFVTHA---HDPRHSFVCPFCQP 162 (175)
T ss_dssp SEEEEE-TTT--EEEEES---S--SS----TT---
T ss_pred CccccCCCCCCCCeECcC---CCCCcCcCCCCCCC
Confidence 456799999985 55422 12256899999983
No 72
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=46.31 E-value=8.1 Score=20.91 Aligned_cols=23 Identities=22% Similarity=0.465 Sum_probs=14.2
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
+|..|++-|+- ..-+|+.||+..
T Consensus 2 ~CP~C~~~V~~--------~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPE--------SAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchh--------hcCcCCCCCCCC
Confidence 46777776632 245677777653
No 73
>PRK11823 DNA repair protein RadA; Provisional
Probab=46.17 E-value=9.6 Score=33.44 Aligned_cols=29 Identities=21% Similarity=0.339 Sum_probs=22.7
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMRG 124 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp~ 124 (140)
.-+|++|+ +....+.|+|+-|+..|.+..
T Consensus 7 ~y~C~~Cg--------~~~~~~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 7 AYVCQECG--------AESPKWLGRCPECGAWNTLVE 35 (446)
T ss_pred eEECCcCC--------CCCcccCeeCcCCCCccceee
Confidence 46777776 455667899999999998865
No 74
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=46.01 E-value=14 Score=22.57 Aligned_cols=22 Identities=18% Similarity=0.471 Sum_probs=14.3
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~ 117 (140)
++|..|+ +.|.. |.+|+|..|.
T Consensus 1 I~CDgCg--~~PI~-----G~RykC~~C~ 22 (43)
T cd02342 1 IQCDGCG--VLPIT-----GPRYKSKVKE 22 (43)
T ss_pred CCCCCCC--CCccc-----ccceEeCCCC
Confidence 3566676 33443 6789998875
No 75
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=43.67 E-value=27 Score=23.33 Aligned_cols=33 Identities=24% Similarity=0.491 Sum_probs=24.8
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMR 123 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp 123 (140)
-++|..|+ |--+-|......-+|..||..---|
T Consensus 19 ~VkCpdC~---N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 19 RVKCPDCG---NEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EEECCCCC---CEEEEeccCceEEEecccccEEEec
Confidence 48899997 5566677777889999999765333
No 76
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=43.21 E-value=16 Score=20.77 Aligned_cols=13 Identities=23% Similarity=0.467 Sum_probs=9.0
Q ss_pred CCCeeecCCCCcE
Q 032449 85 ESGLVRCCCCRGY 97 (140)
Q Consensus 85 ~~~~~RC~~C~aY 97 (140)
..+++||..|+.-
T Consensus 14 ~~~~irC~~CG~R 26 (32)
T PF03604_consen 14 PGDPIRCPECGHR 26 (32)
T ss_dssp TSSTSSBSSSS-S
T ss_pred CCCcEECCcCCCe
Confidence 3567899999753
No 77
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=42.34 E-value=14 Score=26.64 Aligned_cols=37 Identities=16% Similarity=0.099 Sum_probs=27.8
Q ss_pred eecCCCCcEEcCce----eEEeCCcEEEEccCCCCCCCCCC
Q 032449 89 VRCCCCRGYRNPFM----EFVDNGKSFVCNFCGVWMLMRGL 125 (140)
Q Consensus 89 ~RC~~C~aYiNPf~----~~~~~g~~w~C~lC~~~N~lp~~ 125 (140)
--|++|.++|=|.. .+..+.-.|+|--||..--+|-.
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p~~ 97 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYPYG 97 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEeccc
Confidence 45999999877654 44455578999999998877643
No 78
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=42.32 E-value=8.1 Score=22.18 Aligned_cols=28 Identities=32% Similarity=0.701 Sum_probs=17.4
Q ss_pred cCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 91 C~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
|.+|++==.|.-+-...|....||-|+.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~ 28 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGL 28 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHH
Confidence 6777777777777777777778998874
No 79
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=42.16 E-value=15 Score=18.53 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=8.0
Q ss_pred EEEccCCCCC
Q 032449 111 FVCNFCGVWM 120 (140)
Q Consensus 111 w~C~lC~~~N 120 (140)
|.|.+|+..-
T Consensus 1 ~~C~~C~~~f 10 (25)
T PF12874_consen 1 FYCDICNKSF 10 (25)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCCc
Confidence 8999998654
No 80
>PF14353 CpXC: CpXC protein
Probab=41.22 E-value=28 Score=24.91 Aligned_cols=23 Identities=17% Similarity=0.207 Sum_probs=10.7
Q ss_pred CeeecCCCCcEEc---CceeEEeCCc
Q 032449 87 GLVRCCCCRGYRN---PFMEFVDNGK 109 (140)
Q Consensus 87 ~~~RC~~C~aYiN---Pf~~~~~~g~ 109 (140)
-..+|.+|++... |+.-.+...+
T Consensus 37 ~~~~CP~Cg~~~~~~~p~lY~D~~~~ 62 (128)
T PF14353_consen 37 FSFTCPSCGHKFRLEYPLLYHDPEKK 62 (128)
T ss_pred CEEECCCCCCceecCCCEEEEcCCCC
Confidence 3455555555443 4444444433
No 81
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=40.30 E-value=27 Score=19.95 Aligned_cols=30 Identities=20% Similarity=0.380 Sum_probs=17.4
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCCCCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLM 122 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~l 122 (140)
=|..|+..|=| +-+..++. .|.-|+....+
T Consensus 3 FCp~C~nlL~p--~~~~~~~~-~C~~C~Y~~~~ 32 (35)
T PF02150_consen 3 FCPECGNLLYP--KEDKEKRV-ACRTCGYEEPI 32 (35)
T ss_dssp BETTTTSBEEE--EEETTTTE-EESSSS-EEE-
T ss_pred eCCCCCccceE--cCCCccCc-CCCCCCCccCC
Confidence 37777777743 44455445 78888765533
No 82
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=39.67 E-value=17 Score=24.03 Aligned_cols=23 Identities=22% Similarity=0.391 Sum_probs=16.8
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
..-|++|+.... + . +|+.|+...
T Consensus 5 ~~AC~~C~~i~~-------~-~--~Cp~Cgs~~ 27 (64)
T PRK06393 5 YRACKKCKRLTP-------E-K--TCPVHGDEK 27 (64)
T ss_pred hhhHhhCCcccC-------C-C--cCCCCCCCc
Confidence 356999997762 1 1 899999875
No 83
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=38.85 E-value=53 Score=24.58 Aligned_cols=34 Identities=24% Similarity=0.580 Sum_probs=26.4
Q ss_pred eeecCCCCcEEcCceeEEeCCcE--EEEccCCCCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKS--FVCNFCGVWMLMRG 124 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~--w~C~lC~~~N~lp~ 124 (140)
-+.|+.|+. |=..+...++. -.|..||..-.+..
T Consensus 102 yVlC~~C~s---pdT~l~k~~r~~~l~C~ACGa~~~V~~ 137 (138)
T PRK03988 102 YVICPECGS---PDTKLIKEGRIWVLKCEACGAETPVKP 137 (138)
T ss_pred cEECCCCCC---CCcEEEEcCCeEEEEcccCCCCCcCCc
Confidence 489999996 77777776664 57999999887643
No 84
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.14 E-value=21 Score=27.28 Aligned_cols=31 Identities=26% Similarity=0.406 Sum_probs=21.2
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWML 121 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~ 121 (140)
.+--|.+|++-+.-- .+.-.|.||+|...-.
T Consensus 88 q~r~CARCGGrv~lr----sNKv~wvcnlc~k~q~ 118 (169)
T KOG3799|consen 88 QTRFCARCGGRVSLR----SNKVMWVCNLCRKQQE 118 (169)
T ss_pred hhhHHHhcCCeeeec----cCceEEeccCCcHHHH
Confidence 345578898876533 3445899999986543
No 85
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=36.93 E-value=25 Score=25.73 Aligned_cols=28 Identities=18% Similarity=0.267 Sum_probs=20.5
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
.-.+|..|..++-+-. ..+.|+.|+..+
T Consensus 69 ~~~~C~~C~~~~~~e~------~~~~CP~C~s~~ 96 (115)
T COG0375 69 AECWCLDCGQEVELEE------LDYRCPKCGSIN 96 (115)
T ss_pred cEEEeccCCCeecchh------heeECCCCCCCc
Confidence 3589999977766543 345699999766
No 86
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=36.34 E-value=32 Score=28.21 Aligned_cols=28 Identities=21% Similarity=0.390 Sum_probs=19.0
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
--|.+|++-|- ....-+..+|.|+.|..
T Consensus 245 ~pCprCG~~I~--~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 245 EPCLNCKTPIR--RVVVAGRSSHYCPHCQK 272 (272)
T ss_pred CcCCCCCCeeE--EEEECCCccEECcCCcC
Confidence 35889998772 22334567899999963
No 87
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=36.32 E-value=28 Score=20.86 Aligned_cols=29 Identities=21% Similarity=0.527 Sum_probs=20.4
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
..+..|..|+..|-. .....++|..|+..
T Consensus 9 ~~~~~C~~C~~~i~g-----~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWG-----LGKQGYRCSWCGLV 37 (53)
T ss_dssp SSTEB-TTSSSBECS-----SSSCEEEETTTT-E
T ss_pred CCCCCCcccCcccCC-----CCCCeEEECCCCCh
Confidence 457899999999922 34567999999853
No 88
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF15288 zf-CCHC_6: Zinc knuckle
Probab=35.49 E-value=14 Score=22.22 Aligned_cols=11 Identities=27% Similarity=0.887 Sum_probs=8.6
Q ss_pred eecCCCCcEEc
Q 032449 89 VRCCCCRGYRN 99 (140)
Q Consensus 89 ~RC~~C~aYiN 99 (140)
.||.+|++|=+
T Consensus 2 ~kC~~CG~~GH 12 (40)
T PF15288_consen 2 VKCKNCGAFGH 12 (40)
T ss_pred ccccccccccc
Confidence 58999999743
No 90
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=34.96 E-value=18 Score=33.56 Aligned_cols=25 Identities=24% Similarity=0.410 Sum_probs=18.9
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
-.+-+|..|+ |+ .|..|.|+.||..
T Consensus 624 ~~~~~C~~CG-~~--------~g~~~~CP~CG~~ 648 (656)
T PRK08270 624 PTFSICPKHG-YL--------SGEHEFCPKCGEE 648 (656)
T ss_pred CCCcccCCCC-Cc--------CCCCCCCcCCcCc
Confidence 3567899998 44 3568999999944
No 91
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=34.65 E-value=14 Score=25.09 Aligned_cols=14 Identities=36% Similarity=0.657 Sum_probs=5.4
Q ss_pred cEEEEccCCCCCCC
Q 032449 109 KSFVCNFCGVWMLM 122 (140)
Q Consensus 109 ~~w~C~lC~~~N~l 122 (140)
+.|.|++|++.+.+
T Consensus 21 ~~F~CPfC~~~~sV 34 (81)
T PF05129_consen 21 KVFDCPFCNHEKSV 34 (81)
T ss_dssp S----TTT--SS-E
T ss_pred ceEcCCcCCCCCeE
Confidence 57899999988754
No 92
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=34.56 E-value=57 Score=25.70 Aligned_cols=33 Identities=24% Similarity=0.569 Sum_probs=26.2
Q ss_pred eeecCCCCcEEcCceeEEeCCcEE--EEccCCCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSF--VCNFCGVWMLMR 123 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w--~C~lC~~~N~lp 123 (140)
-+.|..|+. |=..+...++.| .|..||..-.+.
T Consensus 98 yV~C~~C~~---pdT~l~k~~~~~~l~C~aCGa~~~v~ 132 (201)
T PRK12336 98 YVICSECGL---PDTRLVKEDRVLMLRCDACGAHRPVK 132 (201)
T ss_pred eEECCCCCC---CCcEEEEcCCeEEEEcccCCCCcccc
Confidence 488999995 777777756654 799999888775
No 93
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=34.47 E-value=23 Score=25.82 Aligned_cols=31 Identities=23% Similarity=0.432 Sum_probs=24.4
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
.-.-+|..|+..+--..+. ...++.|..|+.
T Consensus 121 ~~~~~C~~C~~~~~r~~~~--~~~~~~C~~C~~ 151 (157)
T PF10263_consen 121 KYVYRCPSCGREYKRHRRS--KRKRYRCGRCGG 151 (157)
T ss_pred ceEEEcCCCCCEeeeeccc--chhhEECCCCCC
Confidence 4578999999888777666 456899999983
No 94
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=33.88 E-value=20 Score=25.87 Aligned_cols=14 Identities=36% Similarity=0.712 Sum_probs=11.2
Q ss_pred cEEEEccCCCCCCC
Q 032449 109 KSFVCNFCGVWMLM 122 (140)
Q Consensus 109 ~~w~C~lC~~~N~l 122 (140)
++|.|++|++.+..
T Consensus 21 k~FtCp~Cghe~vs 34 (104)
T COG4888 21 KTFTCPRCGHEKVS 34 (104)
T ss_pred ceEecCccCCeeee
Confidence 68999999988744
No 95
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=33.19 E-value=29 Score=20.17 Aligned_cols=11 Identities=27% Similarity=0.667 Sum_probs=5.8
Q ss_pred CeeecCCCCcE
Q 032449 87 GLVRCCCCRGY 97 (140)
Q Consensus 87 ~~~RC~~C~aY 97 (140)
.+-+|.+|++.
T Consensus 18 ~id~C~~C~G~ 28 (41)
T PF13453_consen 18 EIDVCPSCGGI 28 (41)
T ss_pred EEEECCCCCeE
Confidence 34555555554
No 96
>PRK05580 primosome assembly protein PriA; Validated
Probab=33.06 E-value=52 Score=30.48 Aligned_cols=38 Identities=16% Similarity=0.352 Sum_probs=20.4
Q ss_pred eeecCCCCcEE-cCcee----EEeCCcEEEEccCCCCCCCCCC
Q 032449 88 LVRCCCCRGYR-NPFME----FVDNGKSFVCNFCGVWMLMRGL 125 (140)
Q Consensus 88 ~~RC~~C~aYi-NPf~~----~~~~g~~w~C~lC~~~N~lp~~ 125 (140)
.++|.+|+.-+ +|.|. +....+.-+|..||..-.+|..
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~ 423 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKA 423 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCC
Confidence 45555555433 23332 2234566777777777666543
No 97
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=32.65 E-value=14 Score=26.45 Aligned_cols=28 Identities=29% Similarity=0.407 Sum_probs=18.3
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
...||..|+.-..+-- ..+.|+.|+..+
T Consensus 69 ~~~~C~~Cg~~~~~~~------~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDE------FDFSCPRCGSPD 96 (113)
T ss_dssp -EEEETTTS-EEECHH------CCHH-SSSSSS-
T ss_pred CcEECCCCCCEEecCC------CCCCCcCCcCCC
Confidence 4589999998766542 336799999875
No 98
>PRK11827 hypothetical protein; Provisional
Probab=32.45 E-value=41 Score=21.84 Aligned_cols=33 Identities=15% Similarity=0.509 Sum_probs=24.9
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMR 123 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp 123 (140)
.|+.|..|++=+- ++.+....+|..|+...++.
T Consensus 7 eILaCP~ckg~L~----~~~~~~~Lic~~~~laYPI~ 39 (60)
T PRK11827 7 EIIACPVCNGKLW----YNQEKQELICKLDNLAFPLR 39 (60)
T ss_pred hheECCCCCCcCe----EcCCCCeEECCccCeecccc
Confidence 5889999998553 34556789999999776654
No 99
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=31.89 E-value=26 Score=21.41 Aligned_cols=22 Identities=32% Similarity=0.839 Sum_probs=14.3
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~ 117 (140)
++|..|+. .|. . |.+|+|..|.
T Consensus 1 i~C~~C~~--~~i----~-g~R~~C~~C~ 22 (49)
T cd02338 1 VSCDGCGK--SNF----T-GRRYKCLICY 22 (49)
T ss_pred CCCCCCcC--CCc----E-EeeEEeCCCC
Confidence 46777773 111 1 5789999885
No 100
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=31.54 E-value=73 Score=18.97 Aligned_cols=28 Identities=21% Similarity=0.384 Sum_probs=15.6
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFC 116 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC 116 (140)
=.+|..|+.-|+.---+..++ +..|.-|
T Consensus 26 Cf~C~~C~~~l~~~~~~~~~~-~~~C~~c 53 (58)
T PF00412_consen 26 CFKCSKCGKPLNDGDFYEKDG-KPYCKDC 53 (58)
T ss_dssp TSBETTTTCBTTTSSEEEETT-EEEEHHH
T ss_pred ccccCCCCCccCCCeeEeECC-EEECHHH
Confidence 356777777776554333333 5666544
No 101
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=31.33 E-value=27 Score=31.56 Aligned_cols=26 Identities=19% Similarity=0.295 Sum_probs=12.3
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
..+-+|.+|+- ...+ .+.|+.||..|
T Consensus 489 ~~~~~C~~CG~--------~~~~-~~~CP~CGs~~ 514 (546)
T PF13597_consen 489 PPIDICPDCGY--------IGGE-GDKCPKCGSEN 514 (546)
T ss_dssp --EEEETTT-----------S---EEE-CCC----
T ss_pred cCcccccCCCc--------CCCC-CCCCCCCCCcc
Confidence 34678999983 2233 89999999987
No 102
>PHA00626 hypothetical protein
Probab=31.29 E-value=48 Score=21.50 Aligned_cols=30 Identities=20% Similarity=0.347 Sum_probs=18.6
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCCCC
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMRGL 125 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp~~ 125 (140)
..++||..|+. ....|+|.-|+....-..+
T Consensus 9 ~~Ivrcg~cr~----------~snrYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 9 GNIAKEKTMRG----------WSDDYVCCDCGYNDSKDAF 38 (59)
T ss_pred ceeeeeceecc----------cCcceEcCCCCCeechhhh
Confidence 34566665542 2467999999976644433
No 103
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=31.02 E-value=26 Score=19.62 Aligned_cols=27 Identities=30% Similarity=0.619 Sum_probs=12.9
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
.+.|..|++=-+= .++..|+|+-|++.
T Consensus 2 ~p~Cp~C~se~~y-----~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCPLCGSEYTY-----EDGELLVCPECGHE 28 (30)
T ss_dssp S---TTT-----E-----E-SSSEEETTTTEE
T ss_pred CCCCCCCCCccee-----ccCCEEeCCccccc
Confidence 3567777653221 34578999999863
No 104
>PF08879 WRC: WRC; InterPro: IPR014977 WRC is named after the conserved Trp-Arg-Cys motif, it contains two distinctive features: a putative nuclear localisation signal and a zinc-finger motif (C3H). It is suggested that WRC functions in DNA binding []. ; GO: 0005515 protein binding
Probab=30.92 E-value=23 Score=21.81 Aligned_cols=9 Identities=33% Similarity=1.058 Sum_probs=7.5
Q ss_pred eCCcEEEEc
Q 032449 106 DNGKSFVCN 114 (140)
Q Consensus 106 ~~g~~w~C~ 114 (140)
.+|++|.|.
T Consensus 10 ~DGK~WrC~ 18 (46)
T PF08879_consen 10 NDGKGWRCS 18 (46)
T ss_pred CCCCccccC
Confidence 568999997
No 105
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=30.77 E-value=24 Score=23.04 Aligned_cols=21 Identities=24% Similarity=0.627 Sum_probs=15.3
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
-|++|+..+. . . +|+.|+...
T Consensus 5 AC~~C~~i~~------~--~--~CP~Cgs~~ 25 (61)
T PRK08351 5 ACRHCHYITT------E--D--RCPVCGSRD 25 (61)
T ss_pred hhhhCCcccC------C--C--cCCCCcCCc
Confidence 5889987772 1 1 599999765
No 106
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=30.68 E-value=57 Score=26.72 Aligned_cols=32 Identities=19% Similarity=0.311 Sum_probs=23.1
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMR 123 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp 123 (140)
-|.+|++=|-- ...-+..+|.|+-|...-++.
T Consensus 237 pC~~Cg~~I~~--~~~~gR~ty~Cp~CQ~~~~~~ 268 (269)
T PRK14811 237 PCPRCGTPIEK--IVVGGRGTHFCPQCQPLRPLR 268 (269)
T ss_pred CCCcCCCeeEE--EEECCCCcEECCCCcCCCCCC
Confidence 49999987743 223356799999999876553
No 107
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=30.06 E-value=38 Score=20.17 Aligned_cols=21 Identities=38% Similarity=0.950 Sum_probs=14.6
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~ 117 (140)
+.|..|+. |. .|.+|+|..|.
T Consensus 1 v~Cd~C~~---~i-----~G~ry~C~~C~ 21 (43)
T cd02340 1 VICDGCQG---PI-----VGVRYKCLVCP 21 (43)
T ss_pred CCCCCCCC---cC-----cCCeEECCCCC
Confidence 35777877 22 25689999886
No 108
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=30.01 E-value=50 Score=26.94 Aligned_cols=27 Identities=19% Similarity=0.338 Sum_probs=19.3
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
-|.+|++=|-- ....+..+|.|+.|..
T Consensus 247 pC~~Cg~~I~~--~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 247 PCRRCGTPIEK--IKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCeeEE--EEECCCCcEECcCCCC
Confidence 39999987742 2333567999999975
No 109
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.33 E-value=23 Score=32.77 Aligned_cols=27 Identities=22% Similarity=0.423 Sum_probs=19.9
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
..+-+|..|+ |+ ..|..|.|+.||..+
T Consensus 564 ~~~~iC~~CG-~~-------~~g~~~~CP~CGs~~ 590 (623)
T PRK08271 564 VKITICNDCH-HI-------DKRTGKRCPICGSEN 590 (623)
T ss_pred CCCccCCCCC-Cc-------CCCCCcCCcCCCCcc
Confidence 4568899998 44 245679999999754
No 110
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=29.32 E-value=43 Score=21.34 Aligned_cols=26 Identities=38% Similarity=0.805 Sum_probs=19.5
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
..+..|..|+.+.=| .-.|..||.-+
T Consensus 25 ~~l~~C~~CG~~~~~---------H~vC~~CG~Y~ 50 (57)
T PRK12286 25 PGLVECPNCGEPKLP---------HRVCPSCGYYK 50 (57)
T ss_pred CcceECCCCCCccCC---------eEECCCCCcCC
Confidence 357889999998766 46788887544
No 111
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=28.79 E-value=50 Score=24.01 Aligned_cols=29 Identities=21% Similarity=0.435 Sum_probs=19.9
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWML 121 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~ 121 (140)
++.|.+|.+- |..- +|.-|+|+.|++.-.
T Consensus 2 lp~CP~C~se---ytY~--dg~~~iCpeC~~EW~ 30 (109)
T TIGR00686 2 LPPCPKCNSE---YTYH--DGTQLICPSCLYEWN 30 (109)
T ss_pred CCcCCcCCCc---ceEe--cCCeeECcccccccc
Confidence 4678888742 3322 356899999998764
No 112
>PRK08402 replication factor A; Reviewed
Probab=28.32 E-value=43 Score=28.83 Aligned_cols=44 Identities=20% Similarity=0.364 Sum_probs=27.1
Q ss_pred CeeecCCCCcEEcCceeE--EeCCcEEEEccCCCCCCCC------CCCcccccccccc
Q 032449 87 GLVRCCCCRGYRNPFMEF--VDNGKSFVCNFCGVWMLMR------GLSSVEGQLNLLL 136 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~--~~~g~~w~C~lC~~~N~lp------~~~~~~~~~~~~~ 136 (140)
...+|..|+= ++ +.+...|+|.-|+...... .+.+.-|+..+-|
T Consensus 211 ~y~aCp~CnK------kv~~~~~~~~~~Ce~~~~v~p~~ryil~~~l~D~TG~~~vt~ 262 (355)
T PRK08402 211 VYDACPECRR------KVDYDPATDTWICPEHGEVEPIKITILDFGLDDGTGYIRVTL 262 (355)
T ss_pred eEecCCCCCe------EEEEecCCCCEeCCCCCCcCcceeEEEEEEEEcCCCcEEEEE
Confidence 4688988764 34 3455789999998644332 2455556555443
No 113
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=27.88 E-value=41 Score=21.21 Aligned_cols=24 Identities=38% Similarity=0.860 Sum_probs=17.1
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
.+..|..|+.+.=|+ ..|..||.-
T Consensus 25 ~l~~C~~cG~~~~~H---------~vc~~cG~Y 48 (55)
T TIGR01031 25 TLVVCPNCGEFKLPH---------RVCPSCGYY 48 (55)
T ss_pred cceECCCCCCcccCe---------eECCccCeE
Confidence 578899999976554 566667643
No 114
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.87 E-value=54 Score=29.25 Aligned_cols=20 Identities=15% Similarity=0.443 Sum_probs=13.1
Q ss_pred eCCcEEEEccCCCCCCCCCC
Q 032449 106 DNGKSFVCNFCGVWMLMRGL 125 (140)
Q Consensus 106 ~~g~~w~C~lC~~~N~lp~~ 125 (140)
...+.-+|..||..-.+|..
T Consensus 236 ~~~~~l~Ch~Cg~~~~~~~~ 255 (505)
T TIGR00595 236 KKEGKLRCHYCGYQEPIPKT 255 (505)
T ss_pred cCCCeEEcCCCcCcCCCCCC
Confidence 34556777777777766643
No 115
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=27.82 E-value=66 Score=18.81 Aligned_cols=12 Identities=25% Similarity=0.949 Sum_probs=9.4
Q ss_pred CCcEEEEccCCC
Q 032449 107 NGKSFVCNFCGV 118 (140)
Q Consensus 107 ~g~~w~C~lC~~ 118 (140)
+...|+|+-|+.
T Consensus 22 g~G~~~C~~Cg~ 33 (37)
T smart00778 22 GRGTWFCSVCGA 33 (37)
T ss_pred CCcCEEeCCCCC
Confidence 445799999975
No 116
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.70 E-value=30 Score=32.58 Aligned_cols=25 Identities=28% Similarity=0.545 Sum_probs=18.5
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
..+-+|..|+ |+.-. .|.|+.||..
T Consensus 678 ~~~~~C~~CG-~~~~~--------~~~CP~CG~~ 702 (735)
T PRK07111 678 HPVDRCPVCG-YLGVI--------EDKCPKCGST 702 (735)
T ss_pred CCCeecCCCC-CCCCc--------CccCcCCCCc
Confidence 4568899998 65432 4999999974
No 117
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=27.68 E-value=23 Score=26.26 Aligned_cols=25 Identities=24% Similarity=0.448 Sum_probs=19.9
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEE
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVC 113 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C 113 (140)
..-+|+.|++|++-+-.... +.|+|
T Consensus 14 ~~y~C~~C~thla~~~dliS--ksf~g 38 (122)
T KOG3399|consen 14 RLYSCAHCKTHLARHDDLIS--KSFRG 38 (122)
T ss_pred ceEeccCCcccccchhhccc--ccccc
Confidence 36899999999998877764 56666
No 118
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=27.39 E-value=29 Score=20.30 Aligned_cols=13 Identities=31% Similarity=0.933 Sum_probs=7.7
Q ss_pred CcEEEEccCCCCC
Q 032449 108 GKSFVCNFCGVWM 120 (140)
Q Consensus 108 g~~w~C~lC~~~N 120 (140)
+..|+|+.||..-
T Consensus 4 ~~~YkC~~CGniV 16 (36)
T PF06397_consen 4 GEFYKCEHCGNIV 16 (36)
T ss_dssp TEEEE-TTT--EE
T ss_pred ccEEEccCCCCEE
Confidence 5689999999764
No 119
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=27.07 E-value=30 Score=31.96 Aligned_cols=42 Identities=17% Similarity=0.359 Sum_probs=31.0
Q ss_pred CCeeecCCCCcEEc----CceeEEeCCcEEEEccCCCCCCCCCCCc
Q 032449 86 SGLVRCCCCRGYRN----PFMEFVDNGKSFVCNFCGVWMLMRGLSS 127 (140)
Q Consensus 86 ~~~~RC~~C~aYiN----Pf~~~~~~g~~w~C~lC~~~N~lp~~~~ 127 (140)
.-+.|+..|+-|=. .|-.-++..-+|+|.+|.+.-.+.++..
T Consensus 317 ~~P~r~~~CkHlQcFD~~~~lq~n~~~pTW~CPVC~~~~~~e~l~i 362 (636)
T KOG2169|consen 317 SLPARGHTCKHLQCFDALSYLQMNEQKPTWRCPVCQKAAPFEGLII 362 (636)
T ss_pred ecCCcccccccceecchhhhHHhccCCCeeeCccCCccccccchhh
Confidence 45788888885533 4555567788999999999887766543
No 120
>PRK00420 hypothetical protein; Validated
Probab=27.07 E-value=39 Score=24.59 Aligned_cols=29 Identities=24% Similarity=0.607 Sum_probs=21.5
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCCCCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLM 122 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~l 122 (140)
-.|..|+ .|++++ .+ ....|+.|+..-.+
T Consensus 24 ~~CP~Cg---~pLf~l-k~-g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCG---LPLFEL-KD-GEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCC---Ccceec-CC-CceECCCCCCeeee
Confidence 5688888 577776 33 48999999986544
No 121
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=26.92 E-value=51 Score=25.17 Aligned_cols=35 Identities=29% Similarity=0.578 Sum_probs=20.7
Q ss_pred eeecCCCCc------EEcCceeEEeCCc------EEEEccCCCCCCC
Q 032449 88 LVRCCCCRG------YRNPFMEFVDNGK------SFVCNFCGVWMLM 122 (140)
Q Consensus 88 ~~RC~~C~a------YiNPf~~~~~~g~------~w~C~lC~~~N~l 122 (140)
-+.|.+|+- |||++-+.+..|. .|+|-+|++.+.+
T Consensus 30 kvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~si 76 (161)
T PF05907_consen 30 KVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRESSI 76 (161)
T ss_dssp EEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEE
T ss_pred EEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCccEE
Confidence 388999985 7888877765433 5899999988866
No 122
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=26.86 E-value=53 Score=19.58 Aligned_cols=22 Identities=27% Similarity=0.742 Sum_probs=14.1
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~ 117 (140)
..|..|+.. |.. |.+|.|..|.
T Consensus 5 ~~C~~C~~~--~i~-----g~Ry~C~~C~ 26 (46)
T PF00569_consen 5 YTCDGCGTD--PII-----GVRYHCLVCP 26 (46)
T ss_dssp CE-SSS-SS--SEE-----SSEEEESSSS
T ss_pred eECcCCCCC--cCc-----CCeEECCCCC
Confidence 678888872 221 5789999995
No 123
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=26.50 E-value=81 Score=20.46 Aligned_cols=33 Identities=21% Similarity=0.430 Sum_probs=23.2
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMR 123 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp 123 (140)
-++|..|..-- .-|......-.|..|++.=.-|
T Consensus 11 ~VkCp~C~n~q---~vFsha~t~V~C~~Cg~~L~~P 43 (59)
T PRK00415 11 KVKCPDCGNEQ---VVFSHASTVVRCLVCGKTLAEP 43 (59)
T ss_pred EEECCCCCCeE---EEEecCCcEEECcccCCCcccC
Confidence 38999998654 4455556788999999765333
No 124
>PRK07218 replication factor A; Provisional
Probab=25.94 E-value=34 Score=30.19 Aligned_cols=27 Identities=19% Similarity=0.142 Sum_probs=20.8
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCC
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLM 122 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~l 122 (140)
.-+-||..|+=-| .+|+|+.||.....
T Consensus 295 gli~rCP~C~r~v----------~~~~C~~hG~ve~~ 321 (423)
T PRK07218 295 GLIERCPECGRVI----------QKGQCRSHGAVEGE 321 (423)
T ss_pred cceecCcCccccc----------cCCcCCCCCCcCCe
Confidence 4578999998777 24999999976543
No 125
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=25.78 E-value=12 Score=24.16 Aligned_cols=33 Identities=15% Similarity=0.152 Sum_probs=19.0
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLM 122 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~l 122 (140)
-+||..|.-.+----..- --.-+|+-|+..|.+
T Consensus 4 tiRC~~CnKlLa~a~~~~--yle~KCPrCK~vN~~ 36 (60)
T COG4416 4 TIRCAKCNKLLAEAEGQA--YLEKKCPRCKEVNEF 36 (60)
T ss_pred eeehHHHhHHHHhcccce--eeeecCCccceeeee
Confidence 378888875553211000 013578888888865
No 126
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=25.70 E-value=43 Score=17.50 Aligned_cols=12 Identities=33% Similarity=0.971 Sum_probs=8.7
Q ss_pred CcEEEEccCCCC
Q 032449 108 GKSFVCNFCGVW 119 (140)
Q Consensus 108 g~~w~C~lC~~~ 119 (140)
-+.|.|..|+..
T Consensus 12 ~k~~~C~~C~k~ 23 (26)
T PF13465_consen 12 EKPYKCPYCGKS 23 (26)
T ss_dssp SSSEEESSSSEE
T ss_pred CCCCCCCCCcCe
Confidence 466888888753
No 127
>KOG4784 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.69 E-value=24 Score=30.51 Aligned_cols=35 Identities=17% Similarity=0.246 Sum_probs=27.6
Q ss_pred CCCeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 85 ESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 85 ~~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
..+.+-|++|+++++-++.-+.... |.|.+|...-
T Consensus 181 ~~d~~~C~rC~~~lg~~~~~~~~n~-v~~~~~~v~~ 215 (348)
T KOG4784|consen 181 GNDRVLCSRCKRCLGLFITKDVYNQ-VADALCFVTL 215 (348)
T ss_pred CCCchhhhhhHhhcCcccccchhhh-eecccceEEc
Confidence 3567899999999999876666544 9999997544
No 128
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=25.57 E-value=57 Score=24.22 Aligned_cols=27 Identities=22% Similarity=0.560 Sum_probs=18.4
Q ss_pred eeecCCCCcEEcCceeEEeCC-cEEEEccCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNG-KSFVCNFCGVWM 120 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g-~~w~C~lC~~~N 120 (140)
-..|..|+-=+ ...+ ..|.|.-|+...
T Consensus 34 Y~aC~~C~kkv------~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 34 YPACPGCNKKV------VEEGNGTYRCEKCNKSV 61 (166)
T ss_pred EccccccCccc------EeCCCCcEECCCCCCcC
Confidence 36777776533 3333 689999999874
No 129
>PHA02942 putative transposase; Provisional
Probab=25.54 E-value=43 Score=28.95 Aligned_cols=29 Identities=24% Similarity=0.311 Sum_probs=21.1
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
.--.|..|+...- ...++.|+|.-||...
T Consensus 324 TSq~Cs~CG~~~~-----~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMV-----EIAHRYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCccC-----cCCCCEEECCCCCCEe
Confidence 3478999998542 2245789999999864
No 130
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=25.44 E-value=21 Score=22.09 Aligned_cols=29 Identities=24% Similarity=0.534 Sum_probs=17.5
Q ss_pred ecCCCCcEEcC--ceeEEeCCcEEEEccCCC
Q 032449 90 RCCCCRGYRNP--FMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 90 RC~~C~aYiNP--f~~~~~~g~~w~C~lC~~ 118 (140)
+|..|+--|.| +..+..+.....|+-|+.
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 67777777766 334433335667777765
No 131
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=25.11 E-value=77 Score=20.27 Aligned_cols=27 Identities=22% Similarity=0.437 Sum_probs=21.1
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMR 123 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp 123 (140)
.+-+|.+|+.|== +-+|+.||.....+
T Consensus 4 ~mr~C~~CgvYTL----------k~~CP~CG~~t~~~ 30 (56)
T PRK13130 4 KIRKCPKCGVYTL----------KEICPVCGGKTKNP 30 (56)
T ss_pred cceECCCCCCEEc----------cccCcCCCCCCCCC
Confidence 4788999999832 56899999877665
No 132
>COG1773 Rubredoxin [Energy production and conversion]
Probab=25.09 E-value=42 Score=21.52 Aligned_cols=17 Identities=41% Similarity=0.790 Sum_probs=11.5
Q ss_pred eeEEeCCcEEEEccCCC
Q 032449 102 MEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 102 ~~~~~~g~~w~C~lC~~ 118 (140)
..|.+--..|.|+.|+.
T Consensus 28 T~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 28 TPFEDLPDDWVCPECGV 44 (55)
T ss_pred CchhhCCCccCCCCCCC
Confidence 33444445799999995
No 133
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=24.88 E-value=15 Score=23.11 Aligned_cols=28 Identities=32% Similarity=0.720 Sum_probs=20.8
Q ss_pred cCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 91 CCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 91 C~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
|.+|++--.|.-.-...+..-.||.|+.
T Consensus 2 C~~C~~~~Tp~WR~g~~~~~~LCNaCgl 29 (54)
T cd00202 2 CSNCGTTTTPLWRRGPSGGSTLCNACGL 29 (54)
T ss_pred CCCCCCCCCcccccCCCCcchHHHHHHH
Confidence 7888887777666555567788999984
No 134
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.63 E-value=65 Score=26.50 Aligned_cols=26 Identities=15% Similarity=0.275 Sum_probs=18.6
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~ 117 (140)
-|.+|++=|-- ....+..+|.|+-|.
T Consensus 256 pC~~Cg~~I~~--~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 256 PCRKCGTPIER--IKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCcCCCeeEE--EEECCCccEECCCCc
Confidence 58889887752 233466789999986
No 135
>PF14692 DUF4462: Domain of unknown function (DUF4462)
Probab=24.61 E-value=26 Score=19.52 Aligned_cols=13 Identities=23% Similarity=0.409 Sum_probs=10.4
Q ss_pred EeeccccCCCHHH
Q 032449 41 RCSLNQIPCTENL 53 (140)
Q Consensus 41 R~T~~~iP~t~~l 53 (140)
|++||.+|+...+
T Consensus 5 r~~WN~LpRag~v 17 (28)
T PF14692_consen 5 RFNWNWLPRAGSV 17 (28)
T ss_pred ccccccCcccccc
Confidence 7899999987654
No 136
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=24.61 E-value=96 Score=29.41 Aligned_cols=43 Identities=14% Similarity=0.285 Sum_probs=30.2
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCCCCCcccccc
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMRGLSSVEGQL 132 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp~~~~~~~~~ 132 (140)
.-+.+|.+|-++| .+-...+...|-.||+.-.+|..=..=|..
T Consensus 442 g~v~~Cp~Cd~~l----t~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 442 GYIAECPNCDSPL----TLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred CCcccCCCCCcce----EEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 3466777777664 344566899999999998888655544444
No 137
>KOG1074 consensus Transcriptional repressor SALM [Transcription]
Probab=24.42 E-value=31 Score=33.35 Aligned_cols=42 Identities=17% Similarity=0.275 Sum_probs=31.1
Q ss_pred ccCCCCeeecCCCCcEEcCceeEE------eCCcEEEEccCCCCCCCC
Q 032449 82 DFGESGLVRCCCCRGYRNPFMEFV------DNGKSFVCNFCGVWMLMR 123 (140)
Q Consensus 82 ~~~~~~~~RC~~C~aYiNPf~~~~------~~g~~w~C~lC~~~N~lp 123 (140)
+.......||+-|.-..+.+.... -+-|-|+||+||....-+
T Consensus 347 ~~~~~~khkCr~CakvfgS~SaLqiHlRSHTGERPfqCnvCG~~FSTk 394 (958)
T KOG1074|consen 347 SEKPFFKHKCRFCAKVFGSDSALQIHLRSHTGERPFQCNVCGNRFSTK 394 (958)
T ss_pred CccccccchhhhhHhhcCchhhhhhhhhccCCCCCeeecccccccccc
Confidence 334456789999999999765443 356789999999766444
No 138
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=23.84 E-value=57 Score=19.21 Aligned_cols=21 Identities=29% Similarity=0.735 Sum_probs=14.3
Q ss_pred ecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 90 RCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 90 RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
||..|.... ..|+|--|+..-
T Consensus 1 ~C~~C~~~~----------~l~~CL~C~~~~ 21 (50)
T smart00290 1 RCSVCGTIE----------NLWLCLTCGQVG 21 (50)
T ss_pred CcccCCCcC----------CeEEecCCCCcc
Confidence 577777533 279999988543
No 139
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=23.56 E-value=52 Score=23.69 Aligned_cols=34 Identities=24% Similarity=0.360 Sum_probs=26.1
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMRG 124 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp~ 124 (140)
.=|.+|++.|=|--.- .+..+.|.-|+....+..
T Consensus 3 ~FCp~Cgsll~p~~~~--~~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 3 RFCPKCGSLLYPKKDD--EGGKLVCRKCGYEEEASN 36 (113)
T ss_pred cccCCccCeeEEeEcC--CCcEEECCCCCcchhccc
Confidence 3589999999886543 345999999998887764
No 140
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=23.54 E-value=1.3e+02 Score=25.08 Aligned_cols=38 Identities=16% Similarity=0.348 Sum_probs=30.9
Q ss_pred CCCeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCCC
Q 032449 85 ESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMRG 124 (140)
Q Consensus 85 ~~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp~ 124 (140)
....+.|+=|++-|+---+-.. +-.+|+-|+.-..|.+
T Consensus 62 ~~p~v~CrVCq~~I~i~gk~~Q--hVVkC~~CnEATPIr~ 99 (256)
T PF09788_consen 62 GAPVVTCRVCQSLIDIEGKMHQ--HVVKCSVCNEATPIRN 99 (256)
T ss_pred CCceEEeecCCceecccCccce--eeEECCCCCccccccC
Confidence 3468999999999998766654 6899999998887754
No 141
>PRK04351 hypothetical protein; Provisional
Probab=23.53 E-value=84 Score=23.70 Aligned_cols=31 Identities=23% Similarity=0.304 Sum_probs=21.6
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
-.-||.+|+.-+--.-++ +..++.|..|+..
T Consensus 111 y~Y~C~~Cg~~~~r~Rr~--n~~~yrCg~C~g~ 141 (149)
T PRK04351 111 YLYECQSCGQQYLRKRRI--NTKRYRCGKCRGK 141 (149)
T ss_pred EEEECCCCCCEeeeeeec--CCCcEEeCCCCcE
Confidence 468999998755333333 3478999999854
No 142
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=23.51 E-value=49 Score=16.15 Aligned_cols=10 Identities=30% Similarity=0.989 Sum_probs=7.7
Q ss_pred EEEccCCCCC
Q 032449 111 FVCNFCGVWM 120 (140)
Q Consensus 111 w~C~lC~~~N 120 (140)
|+|..|+..-
T Consensus 1 y~C~~C~~~f 10 (23)
T PF00096_consen 1 YKCPICGKSF 10 (23)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCcc
Confidence 6899998654
No 143
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=23.46 E-value=43 Score=32.90 Aligned_cols=27 Identities=19% Similarity=0.381 Sum_probs=21.3
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCC
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLM 122 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~l 122 (140)
...-||.+|+.| +-+++|+.||.....
T Consensus 623 v~~RKCPkCG~y----------Tlk~rCP~CG~~Te~ 649 (1095)
T TIGR00354 623 IAIRKCPQCGKE----------SFWLKCPVCGELTEQ 649 (1095)
T ss_pred EEEEECCCCCcc----------cccccCCCCCCcccc
Confidence 456899999998 247899999988643
No 144
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=23.23 E-value=37 Score=22.21 Aligned_cols=19 Identities=47% Similarity=0.761 Sum_probs=13.0
Q ss_pred cEEEEccCCCCCCCCCCCcc
Q 032449 109 KSFVCNFCGVWMLMRGLSSV 128 (140)
Q Consensus 109 ~~w~C~lC~~~N~lp~~~~~ 128 (140)
++-+||+||. |+-|++.++
T Consensus 29 k~~VCnlCGF-NP~Phl~E~ 47 (61)
T PF05715_consen 29 KSQVCNLCGF-NPTPHLTEV 47 (61)
T ss_pred hhhhhcccCC-CCCcccccc
Confidence 3567999997 446766653
No 145
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=23.09 E-value=58 Score=27.22 Aligned_cols=28 Identities=18% Similarity=0.434 Sum_probs=20.2
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGV 118 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~ 118 (140)
--|++|++-|---. ..+..+|.|+-|.+
T Consensus 246 epC~~CGt~I~k~~--~~gR~t~~CP~CQ~ 273 (273)
T COG0266 246 EPCRRCGTPIEKIK--LGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCccCCEeEEEE--EcCCcCEeCCCCCC
Confidence 45899999886432 23456899999964
No 146
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=22.80 E-value=25 Score=30.60 Aligned_cols=32 Identities=19% Similarity=0.248 Sum_probs=23.4
Q ss_pred CCCCeeecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 84 GESGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 84 ~~~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
|.+-.--|.+|+.-++|--... ..|+|+ ||..
T Consensus 236 GKYh~~~c~~C~~~~~~~~~~~---~~~~Cp-CG~~ 267 (374)
T TIGR00375 236 GKYHQTACEACGEPAVSEDAET---ACANCP-CGGR 267 (374)
T ss_pred CccchhhhcccCCcCCchhhhh---cCCCCC-CCCc
Confidence 4566778999988777653332 259999 9987
No 147
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.78 E-value=79 Score=22.42 Aligned_cols=33 Identities=18% Similarity=0.456 Sum_probs=23.2
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
.+..|.+|+++ .--+.++.+.-.-.|..|+...
T Consensus 20 t~f~CP~Cge~-~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 20 KIFECPRCGKV-SISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred cEeECCCCCCe-EeeeecCCCcceEECCCCCCcc
Confidence 46789889863 4445566666678899998654
No 148
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.70 E-value=66 Score=24.11 Aligned_cols=25 Identities=28% Similarity=0.817 Sum_probs=18.4
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
.-|..|++ |.++ .+| .-.|++|++.
T Consensus 29 ~hCp~Cg~---PLF~--KdG-~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGT---PLFR--KDG-EVFCPVCGYR 53 (131)
T ss_pred hhCcccCC---ccee--eCC-eEECCCCCce
Confidence 46889987 5554 554 7999999953
No 149
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=22.36 E-value=56 Score=18.38 Aligned_cols=25 Identities=32% Similarity=0.482 Sum_probs=13.7
Q ss_pred CeeecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 87 GLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 87 ~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
.+.||.+|+.+.-| -+-.|+-|+..
T Consensus 10 ~~~rC~~Cg~~~~p--------Pr~~Cp~C~s~ 34 (37)
T PF12172_consen 10 LGQRCRDCGRVQFP--------PRPVCPHCGSD 34 (37)
T ss_dssp EEEE-TTT--EEES----------SEETTTT--
T ss_pred EEEEcCCCCCEecC--------CCcCCCCcCcc
Confidence 46899999998544 24678888754
No 150
>KOG4623 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.31 E-value=31 Score=31.55 Aligned_cols=34 Identities=21% Similarity=0.540 Sum_probs=22.0
Q ss_pred CeeecCCCCcEEc-CceeEEeCCcEEEEccCCCCCCCCC
Q 032449 87 GLVRCCCCRGYRN-PFMEFVDNGKSFVCNFCGVWMLMRG 124 (140)
Q Consensus 87 ~~~RC~~C~aYiN-Pf~~~~~~g~~w~C~lC~~~N~lp~ 124 (140)
.-+-|.-|+.=.- || .+...|+|+.|..-|.+..
T Consensus 27 t~VnCwFCnk~t~vpy----q~rNswTCpsCEQyNgfte 61 (611)
T KOG4623|consen 27 TTVNCWFCNKKTEVPY----QGRNSWTCPSCEQYNGFTE 61 (611)
T ss_pred ceEEEEEecCcceecc----CCCCCCcCCcHHhhCCCCc
Confidence 3466766643211 33 3567899999999996643
No 151
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=22.18 E-value=63 Score=19.66 Aligned_cols=22 Identities=41% Similarity=1.028 Sum_probs=14.1
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~ 117 (140)
++|..|+.. |. .|.+|+|..|.
T Consensus 1 V~Cd~C~~~--pI-----~G~RykC~~C~ 22 (45)
T cd02344 1 VTCDGCQMF--PI-----NGPRFKCRNCD 22 (45)
T ss_pred CCCCCCCCC--CC-----ccCeEECCCCC
Confidence 356777643 22 25789998887
No 152
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.83 E-value=41 Score=24.78 Aligned_cols=36 Identities=17% Similarity=0.395 Sum_probs=22.4
Q ss_pred eeecCCCCcEE-cCceeEEeCCcEEEEccCCCCCCCC
Q 032449 88 LVRCCCCRGYR-NPFMEFVDNGKSFVCNFCGVWMLMR 123 (140)
Q Consensus 88 ~~RC~~C~aYi-NPf~~~~~~g~~w~C~lC~~~N~lp 123 (140)
.+-|..|.++- --.-....+-.+|+|..|+..-.+-
T Consensus 30 ~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 30 KVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred cCcCCCCCccceeeECCccccccccccCCcCcceeee
Confidence 36677777776 1112222335789999999876553
No 153
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=21.81 E-value=20 Score=23.15 Aligned_cols=17 Identities=18% Similarity=0.313 Sum_probs=12.0
Q ss_pred eCCcEEEEccCCCCCCC
Q 032449 106 DNGKSFVCNFCGVWMLM 122 (140)
Q Consensus 106 ~~g~~w~C~lC~~~N~l 122 (140)
.-....+|+-|++..+|
T Consensus 49 i~eg~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 49 IVEGELICPECGREYPI 65 (68)
T ss_dssp TTTTEEEETTTTEEEEE
T ss_pred ccCCEEEcCCCCCEEeC
Confidence 33458999999876644
No 154
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=21.55 E-value=79 Score=18.86 Aligned_cols=24 Identities=33% Similarity=0.836 Sum_probs=16.3
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCG 117 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~ 117 (140)
-.|..|+ .|.++ +.+| +-.|..|+
T Consensus 18 ~~Cp~C~---~PL~~-~k~g-~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCG---TPLMR-DKDG-KIYCVSCG 41 (41)
T ss_pred CccCCCC---CeeEE-ecCC-CEECCCCC
Confidence 3577785 67776 4554 67899885
No 155
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=21.44 E-value=36 Score=22.50 Aligned_cols=23 Identities=22% Similarity=0.605 Sum_probs=16.8
Q ss_pred eecCCCCcEEcCceeEEeCCcEEEEccCCCC
Q 032449 89 VRCCCCRGYRNPFMEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 89 ~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~ 119 (140)
.-|++|+..++. .+=+|+.|+..
T Consensus 5 kAC~~Ck~l~~~--------d~e~CP~Cgs~ 27 (64)
T COG2093 5 KACKNCKRLTPE--------DTEICPVCGST 27 (64)
T ss_pred HHHhhccccCCC--------CCccCCCCCCc
Confidence 358889877653 35679999865
No 156
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=21.38 E-value=62 Score=21.05 Aligned_cols=26 Identities=23% Similarity=0.474 Sum_probs=19.5
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWMLMR 123 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N~lp 123 (140)
+-+|.+|+.|- -+=+|+.||-...+|
T Consensus 5 ~rkC~~cg~YT----------Lke~Cp~CG~~t~~~ 30 (59)
T COG2260 5 IRKCPKCGRYT----------LKEKCPVCGGDTKVP 30 (59)
T ss_pred hhcCcCCCcee----------ecccCCCCCCccccC
Confidence 56899998872 135799999887775
No 157
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=21.24 E-value=74 Score=25.38 Aligned_cols=20 Identities=30% Similarity=0.477 Sum_probs=16.3
Q ss_pred CCeeecCCCCcEEcCceeEEe
Q 032449 86 SGLVRCCCCRGYRNPFMEFVD 106 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~ 106 (140)
..+..|+.|++|..+ -+|.+
T Consensus 33 i~v~~C~~Cg~~~~~-~~W~~ 52 (236)
T PF04981_consen 33 IEVTICPKCGRYRIG-GRWVD 52 (236)
T ss_pred cCceECCCCCCEECC-CEeee
Confidence 468999999999988 55654
No 158
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=21.24 E-value=54 Score=27.68 Aligned_cols=16 Identities=31% Similarity=0.858 Sum_probs=14.0
Q ss_pred eEEeCCcEEEEccCCC
Q 032449 103 EFVDNGKSFVCNFCGV 118 (140)
Q Consensus 103 ~~~~~g~~w~C~lC~~ 118 (140)
.|+.+||.|+|+||..
T Consensus 135 vw~hGGrif~CsfC~~ 150 (314)
T PF06524_consen 135 VWDHGGRIFKCSFCDN 150 (314)
T ss_pred cccCCCeEEEeecCCC
Confidence 4788999999999984
No 159
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=21.22 E-value=54 Score=26.88 Aligned_cols=18 Identities=28% Similarity=0.508 Sum_probs=14.7
Q ss_pred CeeecCCCCc-EEcCceeE
Q 032449 87 GLVRCCCCRG-YRNPFMEF 104 (140)
Q Consensus 87 ~~~RC~~C~a-YiNPf~~~ 104 (140)
.++||.+|++ .|+|-+.|
T Consensus 145 ~~p~C~~Cg~~~lrP~VV~ 163 (250)
T COG0846 145 LIPRCPKCGGPVLRPDVVW 163 (250)
T ss_pred CCCcCccCCCccccCCEEE
Confidence 4789999999 88887655
No 160
>PRK12366 replication factor A; Reviewed
Probab=20.93 E-value=72 Score=29.45 Aligned_cols=29 Identities=28% Similarity=0.599 Sum_probs=21.3
Q ss_pred CCeeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 86 SGLVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 86 ~~~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
.-..+|..|+--|. .+...|.|.-|+...
T Consensus 530 ~~y~aCp~CnkKv~------~~~g~~~C~~c~~~~ 558 (637)
T PRK12366 530 IILYLCPNCRKRVE------EVDGEYICEFCGEVE 558 (637)
T ss_pred EEEecccccCeEeE------cCCCcEECCCCCCCC
Confidence 34689999966442 345689999999873
No 161
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=20.81 E-value=44 Score=29.60 Aligned_cols=35 Identities=17% Similarity=0.472 Sum_probs=24.0
Q ss_pred CCCeeecCCCCcEEcCc-----------eeEEeCCcEEEEccCCCC
Q 032449 85 ESGLVRCCCCRGYRNPF-----------MEFVDNGKSFVCNFCGVW 119 (140)
Q Consensus 85 ~~~~~RC~~C~aYiNPf-----------~~~~~~g~~w~C~lC~~~ 119 (140)
....-+|.-|+-.-.|- ..|++--..|.|+.|+..
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 34567899999655553 345444457999999954
No 162
>smart00704 ZnF_CDGSH CDGSH-type zinc finger. Function unknown.
Probab=20.44 E-value=1.2e+02 Score=17.74 Aligned_cols=18 Identities=22% Similarity=0.368 Sum_probs=12.6
Q ss_pred EeCCcEEEEccCCCCCCCC
Q 032449 105 VDNGKSFVCNFCGVWMLMR 123 (140)
Q Consensus 105 ~~~g~~w~C~lC~~~N~lp 123 (140)
+.++..|.|. |+.....|
T Consensus 9 e~~~~~~lC~-C~~S~~~P 26 (38)
T smart00704 9 EKREKYALCR-CGRSKNFP 26 (38)
T ss_pred cCCCEEEEee-CCCCCCCC
Confidence 3445678887 88877766
No 163
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=20.31 E-value=46 Score=26.76 Aligned_cols=25 Identities=12% Similarity=0.399 Sum_probs=14.6
Q ss_pred cEEcCceeEEeCCcEEEEccCCCCCC
Q 032449 96 GYRNPFMEFVDNGKSFVCNFCGVWML 121 (140)
Q Consensus 96 aYiNPf~~~~~~g~~w~C~lC~~~N~ 121 (140)
.||..+++- .+..+|.|.+|+++..
T Consensus 64 ~~v~~~~~e-~~~~K~~C~lc~KlFk 88 (214)
T PF04959_consen 64 KFVQKNTKE-EDEDKWRCPLCGKLFK 88 (214)
T ss_dssp GGEEEEE-S-SSSEEEEE-SSS-EES
T ss_pred HHHHHHHHH-HcCCEECCCCCCcccC
Confidence 455555533 3567999999997653
No 164
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=20.02 E-value=80 Score=23.41 Aligned_cols=25 Identities=24% Similarity=0.367 Sum_probs=19.9
Q ss_pred eeecCCCCcEEcCceeEEeCCcEEEEccCCCCC
Q 032449 88 LVRCCCCRGYRNPFMEFVDNGKSFVCNFCGVWM 120 (140)
Q Consensus 88 ~~RC~~C~aYiNPf~~~~~~g~~w~C~lC~~~N 120 (140)
-.||.+|+.+.-|= +-.|.-|+...
T Consensus 29 g~kC~~CG~v~~PP--------r~~Cp~C~~~~ 53 (140)
T COG1545 29 GTKCKKCGRVYFPP--------RAYCPKCGSET 53 (140)
T ss_pred EEEcCCCCeEEcCC--------cccCCCCCCCC
Confidence 48999999987764 45688888885
Done!